Re: [PyMOL] Multi-snapshot superimposition
update:
for the realisation I have tried to use sep_state script with python version
so I modified sep_state adding superimposition
# pymol_save.py#
from pymol import cmd
import glob
import re
def save_sep(prefix=''):
obj_list = cmd.get_names("public_objects")
if obj_list:
for i in range(len(obj_list)):
obj_name = "%s%s.pdb" % (prefix, obj_list[i])
cmd.save(obj_name, obj_list[i])
print "Saving %s" % obj_name
else:
print "No objects found"
cmd.extra_fit('name CA', '*', 'super')
cmd.extend('save_sep', save_sep)
and use it with my pdbs
pymol ${output}/*.pdb -ckqr pymol_save.py > ${output}/!temp/rmsf_fit.log
it align ensemble but did not save the resulted pdbs in separate
files. Finally, the same happenes when I open it in Pymol GUI
pymol-2.2.0 *.pdb pymol_save.py
remarkably when I use in this GUI session just a command 'save_sep' it
saves the files within the same directory (Which is ok!)
however cmd.extend('prefix', save_sep)does not work :(
чт, 27 июн. 2019 г. в 11:48, James Starlight :
>
> Dear Pymol users!
>
> I have a folder with many pdb files. I would like to use pymol in
> no-gui mode in order to i)load all pdb within the pymol; ii)
> superimpose each pdb agains the first (top) pdb; iii) save sperimposed
> pdbs into the new folder under the SAME names of pdbs.
>
> Here is model of my script, which should be modified according to the
> indicated commentaries (mostly on the step of saving results).
>
> ${pymol} -c -d "
> from pymol import cmd
> # we open at once all pdbs which have "B-factors" suffix in its name!
> cmd.load('${output}/!temp/B-factors*')
> # it do almost what I want in terms of the superimposition, however
> not all snapshots are aligned properly
> cmd.extra_fit('name CA', '*', 'super')
> # here the most tricky part that should be modified since I need to
> save snapshots using some command keeping its original names!
> cmd.save('output' + '.pdb')
> "
>
> so the task is that I would like to use it in one command rather then
> to put inside the loop (e.g. opening 2 snapshots for each time to make
> mobile, reference superimposition, which is more easy way).
>
> Thank you in advance!
> James
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[PyMOL] Multi-snapshot superimposition
Dear Pymol users!
I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.
Here is model of my script, which should be modified according to the
indicated commentaries (mostly on the step of saving results).
${pymol} -c -d "
from pymol import cmd
# we open at once all pdbs which have "B-factors" suffix in its name!
cmd.load('${output}/!temp/B-factors*')
# it do almost what I want in terms of the superimposition, however
not all snapshots are aligned properly
cmd.extra_fit('name CA', '*', 'super')
# here the most tricky part that should be modified since I need to
save snapshots using some command keeping its original names!
cmd.save('output' + '.pdb')
"
so the task is that I would like to use it in one command rather then
to put inside the loop (e.g. opening 2 snapshots for each time to make
mobile, reference superimposition, which is more easy way).
Thank you in advance!
James
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[PyMOL] set transparency for selected elements of secondary structure
Dear pymol users! I am trying to set transparency based on the secondary structure using pymol selection algebra # set transparency to all helix and sheets but not loops set cartoon_transparency, 0.5, ss H+S which produce the following output PyMOL>set cartoon_transparency, 0.5, ss H+S Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim". but actually do nothing in terms of visualization. Could you suggest me how it would be possible to fix it? Thanks in advance! ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] PDB post-processing and TER records
Awesome, thanks so much Jared for your usefull suggestions!
all the best
james
вт, 25 июн. 2019 г. в 22:00, Jared Sampson :
>
> Hi James - Glad you got it working.
>
> > chains_array = ["A", "B"]
>
> If you want a list of chains without having to hard-code them, try the
> `get_chains` command.
>
> ```
> chains_array = cmd.get_chains()
> ```
>
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
>
> Alternatively, if you want to remove all the chain IDs (which it appears you
> might), you don't need a list of chains at all, and can just do:
>
> ```
> alter all, chain=''
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On June 25, 2019 at 11:48:32 AM, James Starlight (jmsstarli...@gmail.com)
> wrote:
>
> I have got it, it works now!
> in my example the double quotes were not escaped in pymol script :-)
>
> the only (more python-oriented) question, would it be possible to
> indicate chains_array for all letters A-Z (e.g. using some python
> regex, rather just for A and B, chains_array = ["A", "B"], like in my
> example?
>
>
> вт, 25 июн. 2019 г. в 17:22, James Starlight :
> >
> > I actually tried to do like that still defining chains_array = ["A",
> > "B"] inside of pymol script and use external bash loop to loop over
> > pdbs
> > but it does not works ;(
> >
> > #!/bin/bash
> > # this script rename chains in pdb to "empty" chain
> > home=$(pwd)
> > pdb_folder=$home/pdbs
> > output=$home/output
> > rm -r $output
> > mkdir $output
> >
> > #pymol -cQkd "
> > for pdb in "${pdb_folder}"/*.pdb ; do
> > pdb_name2=$(basename "${pdb}")
> > pdb_name="${pdb_name2/pdb}"
> > pymol -c -d "
> > from pymol import cmd
> > chains_array = ["A", "B"]
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
> > cmd.set('pdb_use_ter_records', 1)
> > cmd.set('retain_order', 1)
> > cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
> > " > $output/pymol_${pdb_name}.log
> > done
> >
> > вт, 25 июн. 2019 г. в 16:58, James Starlight :
> > >
> > > yes, actually it is better because we avoid looping!
> > > and how it would be possible to use array provided in the externall shell?
> > >
> > > #!/bin/bash
> > > pdb="final.pdb"
> > > output=$(pwd)
> > >
> > > # array given in bash
> > > chains_array=('A' 'B')
> > >
> > > # chains are cutted by pymol
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> > > cmd.set('pdb_use_ter_records', 1)
> > > cmd.set('retain_order', 1)
> > > cmd.save('output_without'+"".join($chains_array) + '.pdb')
> > > "
> > >
> > > вт, 25 июн. 2019 г. в 16:47, Thomas Holder
> > > :
> > > >
> > > > If you want to rename multiple chains at once, make a selection like
> > > > (chain A+B+C). This list selection syntax is documented here:
> > > > https://pymolwiki.org/index.php/Property_Selectors
> > > >
> > > > cmd.load(pdb)
> > > > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > > > cmd.save('output.pdb')
> > > >
> > > > Cheers,
> > > > Thomas
> > > >
> > > >
> > > > > On Jun 25, 2019, at 4:14 PM, James Starlight
> > > > > wrote:
> > > > >
> > > > > thanks so much Thomas, for this example!
> > > > >
> > > > > Actually, your python script does exactly what my bash script -
> > > > > produces number of pdbs for each of the renamed chain.
> > > > > I would like rather to produce at the end ONE pdb with all chains
> > > > > renamed to empty chain...
> > > > > I guess I need to save the result outside of the loop something like
> > > > > this
> > > > >
> > > > > hop hey lalaley #
> > > > > from pymol import cmd
> > > > > pdb = "Ev_complex_model_final.pdb"
> > > > > chains_array = ["A", "B"] # add more chains in case of more complex
> > > > > pdb
> > > > >
> > > > > # loop over chains to rename it
> > > > > for chain in chains_array:
> > > > > cmd.load(pdb)
> > > > > cmd.alter('chain ' + chain, 'chain=""')
> > > > > cmd.delete('*')
> > > > > ##
> > > > >
> > > > > # save output as pdb
> > > > > # I need to add something in the name of output indicating how much
> > > > > chains have been renamed
> > > > > # like output_withoutAB.pdb
> > > > > cmd.save('output_' + '.pdb')
> > > > >
> > > > > thanks in advance for help!
> > > >
> > > > --
> > > > Thomas Holder
> > > > PyMOL Principal Developer
> > > > Schrödinger, Inc.
> > > >
>
>
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Re: [PyMOL] PDB post-processing and TER records
I have got it, it works now!
in my example the double quotes were not escaped in pymol script :-)
the only (more python-oriented) question, would it be possible to
indicate chains_array for all letters A-Z (e.g. using some python
regex, rather just for A and B, chains_array = ["A", "B"], like in my
example?
вт, 25 июн. 2019 г. в 17:22, James Starlight :
>
> I actually tried to do like that still defining chains_array = ["A",
> "B"] inside of pymol script and use external bash loop to loop over
> pdbs
> but it does not works ;(
>
> #!/bin/bash
> # this script rename chains in pdb to "empty" chain
> home=$(pwd)
> pdb_folder=$home/pdbs
> output=$home/output
> rm -r $output
> mkdir $output
>
> #pymol -cQkd "
> for pdb in "${pdb_folder}"/*.pdb ; do
> pdb_name2=$(basename "${pdb}")
> pdb_name="${pdb_name2/pdb}"
> pymol -c -d "
> from pymol import cmd
> chains_array = ["A", "B"]
> cmd.load('${pdb}')
> cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
> " > $output/pymol_${pdb_name}.log
> done
>
> вт, 25 июн. 2019 г. в 16:58, James Starlight :
> >
> > yes, actually it is better because we avoid looping!
> > and how it would be possible to use array provided in the externall shell?
> >
> > #!/bin/bash
> > pdb="final.pdb"
> > output=$(pwd)
> >
> > # array given in bash
> > chains_array=('A' 'B')
> >
> > # chains are cutted by pymol
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> > cmd.set('pdb_use_ter_records', 1)
> > cmd.set('retain_order', 1)
> > cmd.save('output_without'+"".join($chains_array) + '.pdb')
> > "
> >
> > вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
> > >
> > > If you want to rename multiple chains at once, make a selection like
> > > (chain A+B+C). This list selection syntax is documented here:
> > > https://pymolwiki.org/index.php/Property_Selectors
> > >
> > > cmd.load(pdb)
> > > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > > cmd.save('output.pdb')
> > >
> > > Cheers,
> > > Thomas
> > >
> > >
> > > > On Jun 25, 2019, at 4:14 PM, James Starlight
> > > > wrote:
> > > >
> > > > thanks so much Thomas, for this example!
> > > >
> > > > Actually, your python script does exactly what my bash script -
> > > > produces number of pdbs for each of the renamed chain.
> > > > I would like rather to produce at the end ONE pdb with all chains
> > > > renamed to empty chain...
> > > > I guess I need to save the result outside of the loop something like
> > > > this
> > > >
> > > > hop hey lalaley #
> > > > from pymol import cmd
> > > > pdb = "Ev_complex_model_final.pdb"
> > > > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> > > >
> > > > # loop over chains to rename it
> > > > for chain in chains_array:
> > > >cmd.load(pdb)
> > > >cmd.alter('chain ' + chain, 'chain=""')
> > > >cmd.delete('*')
> > > > ##
> > > >
> > > > # save output as pdb
> > > > # I need to add something in the name of output indicating how much
> > > > chains have been renamed
> > > > # like output_withoutAB.pdb
> > > > cmd.save('output_' + '.pdb')
> > > >
> > > > thanks in advance for help!
> > >
> > > --
> > > Thomas Holder
> > > PyMOL Principal Developer
> > > Schrödinger, Inc.
> > >
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Re: [PyMOL] PDB post-processing and TER records
I actually tried to do like that still defining chains_array = ["A",
"B"] inside of pymol script and use external bash loop to loop over
pdbs
but it does not works ;(
#!/bin/bash
# this script rename chains in pdb to "empty" chain
home=$(pwd)
pdb_folder=$home/pdbs
output=$home/output
rm -r $output
mkdir $output
#pymol -cQkd "
for pdb in "${pdb_folder}"/*.pdb ; do
pdb_name2=$(basename "${pdb}")
pdb_name="${pdb_name2/pdb}"
pymol -c -d "
from pymol import cmd
chains_array = ["A", "B"]
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
" > $output/pymol_${pdb_name}.log
done
вт, 25 июн. 2019 г. в 16:58, James Starlight :
>
> yes, actually it is better because we avoid looping!
> and how it would be possible to use array provided in the externall shell?
>
> #!/bin/bash
> pdb="final.pdb"
> output=$(pwd)
>
> # array given in bash
> chains_array=('A' 'B')
>
> # chains are cutted by pymol
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> cmd.save('output_without'+"".join($chains_array) + '.pdb')
> "
>
> вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
> >
> > If you want to rename multiple chains at once, make a selection like (chain
> > A+B+C). This list selection syntax is documented here:
> > https://pymolwiki.org/index.php/Property_Selectors
> >
> > cmd.load(pdb)
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > cmd.save('output.pdb')
> >
> > Cheers,
> > Thomas
> >
> >
> > > On Jun 25, 2019, at 4:14 PM, James Starlight
> > > wrote:
> > >
> > > thanks so much Thomas, for this example!
> > >
> > > Actually, your python script does exactly what my bash script -
> > > produces number of pdbs for each of the renamed chain.
> > > I would like rather to produce at the end ONE pdb with all chains
> > > renamed to empty chain...
> > > I guess I need to save the result outside of the loop something like this
> > >
> > > hop hey lalaley #
> > > from pymol import cmd
> > > pdb = "Ev_complex_model_final.pdb"
> > > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> > >
> > > # loop over chains to rename it
> > > for chain in chains_array:
> > >cmd.load(pdb)
> > >cmd.alter('chain ' + chain, 'chain=""')
> > >cmd.delete('*')
> > > ##
> > >
> > > # save output as pdb
> > > # I need to add something in the name of output indicating how much
> > > chains have been renamed
> > > # like output_withoutAB.pdb
> > > cmd.save('output_' + '.pdb')
> > >
> > > thanks in advance for help!
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
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Re: [PyMOL] PDB post-processing and TER records
yes, actually it is better because we avoid looping!
and how it would be possible to use array provided in the externall shell?
#!/bin/bash
pdb="final.pdb"
output=$(pwd)
# array given in bash
chains_array=('A' 'B')
# chains are cutted by pymol
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join($chains_array) + '.pdb')
"
вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
>
> If you want to rename multiple chains at once, make a selection like (chain
> A+B+C). This list selection syntax is documented here:
> https://pymolwiki.org/index.php/Property_Selectors
>
> cmd.load(pdb)
> cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> cmd.save('output.pdb')
>
> Cheers,
> Thomas
>
>
> > On Jun 25, 2019, at 4:14 PM, James Starlight wrote:
> >
> > thanks so much Thomas, for this example!
> >
> > Actually, your python script does exactly what my bash script -
> > produces number of pdbs for each of the renamed chain.
> > I would like rather to produce at the end ONE pdb with all chains
> > renamed to empty chain...
> > I guess I need to save the result outside of the loop something like this
> >
> > hop hey lalaley #
> > from pymol import cmd
> > pdb = "Ev_complex_model_final.pdb"
> > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> >
> > # loop over chains to rename it
> > for chain in chains_array:
> >cmd.load(pdb)
> >cmd.alter('chain ' + chain, 'chain=""')
> >cmd.delete('*')
> > ##
> >
> > # save output as pdb
> > # I need to add something in the name of output indicating how much
> > chains have been renamed
> > # like output_withoutAB.pdb
> > cmd.save('output_' + '.pdb')
> >
> > thanks in advance for help!
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
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Re: [PyMOL] PDB post-processing and TER records
in python version I have got it
# to be run with PyMOL:
#pymol -ckqr pymol_cut_off.py
cut_off.py #
from pymol import cmd
pdb = "final.pdb"
chains_array = ["A", "B"] # two chains will be cuted
for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join(chains_array) + '.pdb')
now the question would it be possible to do the same but in my bash script?
вт, 25 июн. 2019 г. в 16:20, James Starlight :
>
> OK Lorenzo, thank you !
>
> As an alternative question, would it be possible to put that loop
> while renaming of the chains in the processed PBD within the bash
> loop?
>
> Here is an idea
>
> #!/bin/bash
> # this script rename chains in pdb to "empty" chain
> pdb="my.pdb"
> output=$(pwd)
>
> # chain array is provided in a shell array
> chains=('A' 'B')
>
> # create several pdbs without individual chains
> #pymol -cQkd "
> pymol -c -d "
> # I need to add loop within PYMOL over the elements of external arrays
> for chains
> # mb for i in chains:
> cmd.load('${pdb}')
> cmd.alter('(chain $i)', 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> # close the loop and save final output as 1 pdb
> cmd.save('${output}/output_withoutAB.pdb','all')
> "
>
> вт, 25 июн. 2019 г. в 16:14, James Starlight :
> >
> > thanks so much Thomas, for this example!
> >
> > Actually, your python script does exactly what my bash script -
> > produces number of pdbs for each of the renamed chain.
> > I would like rather to produce at the end ONE pdb with all chains
> > renamed to empty chain...
> > I guess I need to save the result outside of the loop something like this
> >
> > hop hey lalaley #
> > from pymol import cmd
> > pdb = "Ev_complex_model_final.pdb"
> > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> >
> > # loop over chains to rename it
> > for chain in chains_array:
> > cmd.load(pdb)
> > cmd.alter('chain ' + chain, 'chain=""')
> > cmd.delete('*')
> > ##
> >
> > # save output as pdb
> > # I need to add something in the name of output indicating how much
> > chains have been renamed
> > # like output_withoutAB.pdb
> > cmd.save('output_' + '.pdb')
> >
> > thanks in advance for help!
> >
> > вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
> > >
> > > > generally if I integrate a pymol silent script inside my
> > > > bash script, I do not need to use cmd.* syntax, right?
> > >
> > > Correct. The -d argument takes PyMOL commands, like a .pml script. Python
> > > syntax is optional.
> > >
> > > Python syntax (cmd.*) is necessary and most useful if you write a Python
> > > script (.py extension) and run that with PyMOL. You could write your
> > > multi-chains loop as a Python script:
> > >
> > > example.py ##
> > > from pymol import cmd
> > > pdb = "my.pdb"
> > > chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
> > >
> > > for chain in chains_array:
> > > cmd.load(pdb)
> > > cmd.alter('chain ' + chain, 'chain=""')
> > > cmd.save('output_' + chain + '.pdb')
> > > cmd.delete('*')
> > > ##
> > >
> > > Then run it with PyMOL:
> > > pymol -ckqr example.py
> > >
> > > See also:
> > > https://pymolwiki.org/index.php/Launching_From_a_Script
> > > https://pymolwiki.org/index.php/Python_Integration
> > >
> > > Cheers,
> > > Thomas
> > >
> > > > On Jun 25, 2019, at 3:08 PM, James Starlight
> > > > wrote:
> > > >
> > > > one extra programming question:
> > > >
> > > > imagine now in my pdb I have severals chain which I would like to
> > > > rename to blank chain.
> > > >
> > > > I can do it simply like this
> > > > # a case for 3 chains to be renamed
> > > >
> > > > #!/bin/bash
> > > > pdb="my.pdb"
> > > > output=$(pwd)
> > > > pymol -c -d "
> > > > cmd.load('${pdb}')
> > > >
Re: [PyMOL] PDB post-processing and TER records
OK Lorenzo, thank you !
As an alternative question, would it be possible to put that loop
while renaming of the chains in the processed PBD within the bash
loop?
Here is an idea
#!/bin/bash
# this script rename chains in pdb to "empty" chain
pdb="my.pdb"
output=$(pwd)
# chain array is provided in a shell array
chains=('A' 'B')
# create several pdbs without individual chains
#pymol -cQkd "
pymol -c -d "
# I need to add loop within PYMOL over the elements of external arrays
for chains
# mb for i in chains:
cmd.load('${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
# close the loop and save final output as 1 pdb
cmd.save('${output}/output_withoutAB.pdb','all')
"
вт, 25 июн. 2019 г. в 16:14, James Starlight :
>
> thanks so much Thomas, for this example!
>
> Actually, your python script does exactly what my bash script -
> produces number of pdbs for each of the renamed chain.
> I would like rather to produce at the end ONE pdb with all chains
> renamed to empty chain...
> I guess I need to save the result outside of the loop something like this
>
> hop hey lalaley #
> from pymol import cmd
> pdb = "Ev_complex_model_final.pdb"
> chains_array = ["A", "B"] # add more chains in case of more complex pdb
>
> # loop over chains to rename it
> for chain in chains_array:
> cmd.load(pdb)
> cmd.alter('chain ' + chain, 'chain=""')
> cmd.delete('*')
> ##
>
> # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_' + '.pdb')
>
> thanks in advance for help!
>
> вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
> >
> > > generally if I integrate a pymol silent script inside my
> > > bash script, I do not need to use cmd.* syntax, right?
> >
> > Correct. The -d argument takes PyMOL commands, like a .pml script. Python
> > syntax is optional.
> >
> > Python syntax (cmd.*) is necessary and most useful if you write a Python
> > script (.py extension) and run that with PyMOL. You could write your
> > multi-chains loop as a Python script:
> >
> > example.py ##
> > from pymol import cmd
> > pdb = "my.pdb"
> > chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
> >
> > for chain in chains_array:
> > cmd.load(pdb)
> > cmd.alter('chain ' + chain, 'chain=""')
> > cmd.save('output_' + chain + '.pdb')
> > cmd.delete('*')
> > ##
> >
> > Then run it with PyMOL:
> > pymol -ckqr example.py
> >
> > See also:
> > https://pymolwiki.org/index.php/Launching_From_a_Script
> > https://pymolwiki.org/index.php/Python_Integration
> >
> > Cheers,
> > Thomas
> >
> > > On Jun 25, 2019, at 3:08 PM, James Starlight
> > > wrote:
> > >
> > > one extra programming question:
> > >
> > > imagine now in my pdb I have severals chain which I would like to
> > > rename to blank chain.
> > >
> > > I can do it simply like this
> > > # a case for 3 chains to be renamed
> > >
> > > #!/bin/bash
> > > pdb="my.pdb"
> > > output=$(pwd)
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('(chain A)', 'chain=\"\"')
> > > cmd.alter('(chain B)', 'chain=\"\"')
> > > cmd.alter('(chain C)', 'chain=\"\"')
> > > cmd.save('${output}/output.pdb','all')
> > > "
> > >
> > > or for multi-chain protein I can alternatively create external loop,
> > > thus running pymol 3 times iteratively (which is not good realization)
> > > providin array info from external shell session
> > >
> > > # this example save 7 different pdbs renaming one chain in each of them
> > > #!/bin/bash
> > > pdb="my.pdb"
> > > output=$(pwd)
> > > chains_arrays=( A B C D E F G )
> > >
> > > for i in "$chains_array[@]}"; do
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('(chain $i)', 'chain=\"\"')
> > > cmd.save('${output}/output_$i.pdb','all')
> > > "
> > > done
> > >
> > > would it be possible rather to make an array and loop inside the pymol
> > > to ren
Re: [PyMOL] PDB post-processing and TER records
thanks so much Thomas, for this example!
Actually, your python script does exactly what my bash script -
produces number of pdbs for each of the renamed chain.
I would like rather to produce at the end ONE pdb with all chains
renamed to empty chain...
I guess I need to save the result outside of the loop something like this
hop hey lalaley #
from pymol import cmd
pdb = "Ev_complex_model_final.pdb"
chains_array = ["A", "B"] # add more chains in case of more complex pdb
# loop over chains to rename it
for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')
cmd.delete('*')
##
# save output as pdb
# I need to add something in the name of output indicating how much
chains have been renamed
# like output_withoutAB.pdb
cmd.save('output_' + '.pdb')
thanks in advance for help!
вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
>
> > generally if I integrate a pymol silent script inside my
> > bash script, I do not need to use cmd.* syntax, right?
>
> Correct. The -d argument takes PyMOL commands, like a .pml script. Python
> syntax is optional.
>
> Python syntax (cmd.*) is necessary and most useful if you write a Python
> script (.py extension) and run that with PyMOL. You could write your
> multi-chains loop as a Python script:
>
> example.py ##
> from pymol import cmd
> pdb = "my.pdb"
> chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
>
> for chain in chains_array:
> cmd.load(pdb)
> cmd.alter('chain ' + chain, 'chain=""')
> cmd.save('output_' + chain + '.pdb')
> cmd.delete('*')
> ##
>
> Then run it with PyMOL:
> pymol -ckqr example.py
>
> See also:
> https://pymolwiki.org/index.php/Launching_From_a_Script
> https://pymolwiki.org/index.php/Python_Integration
>
> Cheers,
> Thomas
>
> > On Jun 25, 2019, at 3:08 PM, James Starlight wrote:
> >
> > one extra programming question:
> >
> > imagine now in my pdb I have severals chain which I would like to
> > rename to blank chain.
> >
> > I can do it simply like this
> > # a case for 3 chains to be renamed
> >
> > #!/bin/bash
> > pdb="my.pdb"
> > output=$(pwd)
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('(chain A)', 'chain=\"\"')
> > cmd.alter('(chain B)', 'chain=\"\"')
> > cmd.alter('(chain C)', 'chain=\"\"')
> > cmd.save('${output}/output.pdb','all')
> > "
> >
> > or for multi-chain protein I can alternatively create external loop,
> > thus running pymol 3 times iteratively (which is not good realization)
> > providin array info from external shell session
> >
> > # this example save 7 different pdbs renaming one chain in each of them
> > #!/bin/bash
> > pdb="my.pdb"
> > output=$(pwd)
> > chains_arrays=( A B C D E F G )
> >
> > for i in "$chains_array[@]}"; do
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('(chain $i)', 'chain=\"\"')
> > cmd.save('${output}/output_$i.pdb','all')
> > "
> > done
> >
> > would it be possible rather to make an array and loop inside the pymol
> > to rename all chains into the blank chain during one execution of
> > pymol?
> >
> > Thanks in advance!
> >
> > вт, 25 июн. 2019 г. в 14:50, James Starlight :
> >>
> >> I have got the idea!
> >> thank you so much Thomas!
> >> One question: generally if I integrate a pymol silent script inside my
> >> bash script, I do not need to use cmd.* syntax, right? In what cases
> >> cmd.* sytax might be usefull?
> >>
> >> Thank you again!
> >>
> >> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
> >>>
> >>>
> >>>> On Jun 25, 2019, at 11:48 AM, James Starlight
> >>>> wrote:
> >>>>
> >>>> so what I need is just to update my pymol, keep using the same command?
> >>>
> >>> Yes
> >>>
> >>>> P.S.would the following integration of the code into bash script be
> >>>> usefull to remove chains in no gui mode?
> >>>>
> >>>> pymol -cQkd "
> >>>> from pymol import cmd
> >>>> fetch $pdb, type=pdb, tmp
> >>>> cmd.alter('(chain A)',chain='')
> >>>> "
> >>>> I am not sure wh
Re: [PyMOL] PDB post-processing and TER records
one extra programming question:
imagine now in my pdb I have severals chain which I would like to
rename to blank chain.
I can do it simply like this
# a case for 3 chains to be renamed
#!/bin/bash
pdb="my.pdb"
output=$(pwd)
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('(chain A)', 'chain=\"\"')
cmd.alter('(chain B)', 'chain=\"\"')
cmd.alter('(chain C)', 'chain=\"\"')
cmd.save('${output}/output.pdb','all')
"
or for multi-chain protein I can alternatively create external loop,
thus running pymol 3 times iteratively (which is not good realization)
providin array info from external shell session
# this example save 7 different pdbs renaming one chain in each of them
#!/bin/bash
pdb="my.pdb"
output=$(pwd)
chains_arrays=( A B C D E F G )
for i in "$chains_array[@]}"; do
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.save('${output}/output_$i.pdb','all')
"
done
would it be possible rather to make an array and loop inside the pymol
to rename all chains into the blank chain during one execution of
pymol?
Thanks in advance!
вт, 25 июн. 2019 г. в 14:50, James Starlight :
>
> I have got the idea!
> thank you so much Thomas!
> One question: generally if I integrate a pymol silent script inside my
> bash script, I do not need to use cmd.* syntax, right? In what cases
> cmd.* sytax might be usefull?
>
> Thank you again!
>
> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
> >
> >
> > > On Jun 25, 2019, at 11:48 AM, James Starlight
> > > wrote:
> > >
> > > so what I need is just to update my pymol, keep using the same command?
> >
> > Yes
> >
> > > P.S.would the following integration of the code into bash script be
> > > usefull to remove chains in no gui mode?
> > >
> > > pymol -cQkd "
> > > from pymol import cmd
> > > fetch $pdb, type=pdb, tmp
> > > cmd.alter('(chain A)',chain='')
> > > "
> > > I am not sure whether I used here cmd.alter in correct way ..
> >
> >
> > With fetch, use "async=0" or use Python syntax. And keyword arguments
> > (type=) must be after positional arguments (tmp).
> >
> > It's easier if you don't use Python syntax for alter, otherwise you'll need
> > three levels of nested quotes, which gets ugly:
> >
> > pymol -cQkd "
> > fetch $pdb, tmp, type=pdb, async=0
> > alter (chain A), chain=''
> > "
> >
> > With Python syntax (note the ugly escaping of quotes):
> >
> > pymol -cQkd "
> > cmd.fetch('$pdb', 'tmp', type='pdb')
> > cmd.alter('(chain A)', 'chain=\"\"')
> > "
> >
> > Cheers,
> > Thomas
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
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[PyMOL] PDB post-processing and TER records
Dear Pymol Users! I need to process input PDB via pymol (this time no need to do it via no-gui mode!!) to remove chain id from PDB. I am using alter command to do it with the following syntax #rename chain A to phantom chain :-) alter (chain A),chain='' the problem that in my initial PDBs there are many TER records (e.g. to separate protein from ligand etc), which should be keeped after such post-processing in the form of original PDB (with chain A). I have tried to do this before saving of the PDB get pdb_use_ter_records however, as the result, all the TER records were removed from the processed pdb. How I could fix it? Many thanks in advance! ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] counting number of standard amino acids in PDB
Thank so much Jared!
So here is modified script:
#!/bin/bash
pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
LENGTH="$(pymol -cQ -d "
from pymol import cmd
load ${pdb}, tmp
sel = 'tmp and polymer'
print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
")"
echo $LENGTH
I guess it's a problem with the -cQ flag because without it your
script gives me the full output, while I echoes the variable:
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1. Copyright (c)
Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano,
Ph.D. PyMOL is user-supported open-source software. Although some
versions are freely available, PyMOL is not in the public domain. If
PyMOL is helpful in your work or study, then please volunteer support
for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support
subscription. More information can be found at "http://www.pymol.org;.
Enter "help" for a list of commands. Enter "help " for
information on a specific command. Hit ESC anytime to toggle between
text and graphics. Command mode. No graphics front end. Detected 20
CPU cores. Enabled multithreaded rendering. PyMOL> PyMOL>from pymol
import cmd PyMOL>load ./NpXynWT_apo_340K_MD_multi_0434.pdb, tmp
CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp".
PyMOL>sel = 'tmp and polymer' PyMOL>print(len(set([(i.chain, i.resi,
i.resn) for i in cmd.get_model(sel).atom]))) 219 PyMOL: normal program
termination.
however with -cQ it gives me nothing :-)
Hey Blaine,
your script is very usefull but it does not work in my case.
1) fetch command gives me an error (which is not the case of "load"
probably because I have outdated pymol).
2) I need to load pdbs inside of my shell script, meaning that I am
looping a folder by bash routine and use it then with pymol to measure
the length of PDB and save it as the variable (in bash!!), which is
expected to be used on the next step...
james
пн, 24 июн. 2019 г. в 18:53, Jared Sampson :
>
> Hi James -
>
> Try this, assigning to new variable LENGTH by using -Q flag to suppress other
> output, and running in a subshell (untested, and assuming Bash):
>
> ```
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> LENGTH=$(pymol -cQ -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> ")
> ```
>
> Hopefully that works, or at least gives you an idea of how it might be done.
>
> Best,
> Jared
>
>
> On June 24, 2019 at 12:08:07 PM, James Starlight (jmsstarli...@gmail.com)
> wrote:
>
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> pymol -c -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> "
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Re: [PyMOL] counting number of standard amino acids in PDB
hi Jared,
I have tried to use your script putting it into my test.sh script
I only changed the selection statement in sel = 'tmp and
polymer.protein' instead of sel = 'tmp and chain A and
polymer.protein'
since in my protein there is no chains assigned
pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
pymol -c -d "
from pymol import cmd
load ${pdb}, tmp
sel = 'tmp and polymer.protein'
print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
"
execution of that sh script gave me the following error
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org;.
Enter "help" for a list of commands.
Enter "help " for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Command mode. No graphics front end.
Detected 20 CPU cores. Enabled multithreaded rendering.
PyMOL>from pymol import cmd
PyMOL>load ./NpXynWT_apo_340K_MD_multi_0434.pdb, tmp
CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp".
PyMOL>sel = 'tmp and polymer.protein'
PyMOL>print(len(set([(i.chain, i.resi, i.resn) for i in
cmd.get_model(sel).atom])))
Selector-Error: Invalid selection name "polymer.protein".
( tmp and polymer.protein )<--
PyMOL: normal program termination.
пн, 24 июн. 2019 г. в 17:44, Jared Sampson :
>
> Hi James -
>
> You can give multiple commands by leaving the quote open as you did on the
> first line (see Thomas' post from a day or two ago), but the `print`
> statement, even though it is valid Python 2, will not work across line breaks
> as written unless inside a `python` / `python end` block (also unless you are
> using Python 2!). I would suggest performing the print operation on a single
> line. You'll also need to load your model and specify the selection using
> PyMOL selection syntax such that it includes only protein residues (e.g.
> polymer.protein). For example, for my PyMOL running Python 3.7 (which
> requires using the `print()` function, i.e. with parentheses), the following
> command works:
>
> ```
> pymol -cQkd "
> from pymol import cmd
> load my_structure.pdb, tmp
> sel = 'tmp and chain A and polymer.protein'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> "
> ```
>
> Here I put in the -Q option which suppresses all of PyMOL's normal output, as
> well as -k, which prevents it from loading the .pymolrc file (for speed,
> mostly). Also note the quotes in the `sel` variable assignment must be
> single quotes to avoid closing the shell string.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
>
> On June 24, 2019 at 10:25:22 AM, James Starlight (jmsstarli...@gmail.com)
> wrote:
>
> Thank you, Jared!
> how do you think would it be possible to run this command from no-gui pymol?
>
> pymol -c -d "
> from pymol import cmd
> print len( set( [(i.chain,i.resi,i.resn) for i in
> cmd.get_model(selection).atom] ) )
> "
>
> ?
>
> пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
> >
> > Hi James -
> >
> > Do any of the options from this previous BB discussion help?
> >
> > https://sourceforge.net/p/pymol/mailman/message/28466955/
> >
> > Cheers,
> > Jared
> >
> >
> > On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com)
> > wrote:
> >
> > Dear Pymol Users,
> >
> > that is not very related to pymol question but however probably it can
> > be solved via pymol as well ;-)
> >
> > I am looking for some script (e.g. via running in pymol no-gui), which
> > will count the number of standard amino acid residues in the given
> > PDB. E.g. for particular pdb consisted of 9 residues complexed with
> > part of the ligand I need to print the value of 9 (the end value of
> > 6th column before TER)
> >
> > ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N
> > ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C
> > ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C
> > ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O
> > ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C
> > ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C
> > ATOM 7 SD MET A 1 28.713
Re: [PyMOL] counting number of standard amino acids in PDB
i also tried more simple sollution directly from terminal but it
doesn't work also
pymol -c -d "
from pymol import cmd
cmd.load('my.pdb')
cmd.count_atoms('n. CA')
"
actually what I do need is to compute number of residues and store it
in a variable (inside of my shell script)
пн, 24 июн. 2019 г. в 16:25, James Starlight :
>
> Thank you, Jared!
> how do you think would it be possible to run this command from no-gui pymol?
>
> pymol -c -d "
> from pymol import cmd
> print len( set( [(i.chain,i.resi,i.resn) for i in
> cmd.get_model(selection).atom] ) )
> "
>
> ?
>
> пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
> >
> > Hi James -
> >
> > Do any of the options from this previous BB discussion help?
> >
> > https://sourceforge.net/p/pymol/mailman/message/28466955/
> >
> > Cheers,
> > Jared
> >
> >
> > On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com)
> > wrote:
> >
> > Dear Pymol Users,
> >
> > that is not very related to pymol question but however probably it can
> > be solved via pymol as well ;-)
> >
> > I am looking for some script (e.g. via running in pymol no-gui), which
> > will count the number of standard amino acid residues in the given
> > PDB. E.g. for particular pdb consisted of 9 residues complexed with
> > part of the ligand I need to print the value of 9 (the end value of
> > 6th column before TER)
> >
> > ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N
> > ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C
> > ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C
> > ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O
> > ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C
> > ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C
> > ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S
> > ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C
> > ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N
> > ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C
> > ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C
> > ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O
> > ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C
> > ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C
> > ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C
> > ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C
> > ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+
> > ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N
> > ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C
> > ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C
> > ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O
> > ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C
> > ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C
> > ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C
> > ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C
> > ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C
> > ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C
> > ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C
> > ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N
> > ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C
> > ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C
> > ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O
> > ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C
> > ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C
> > ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O
> > ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N
> > ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C
> > ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C
> > ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O
> > ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C
> > ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C
> > ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C
> > ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N
> > ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C
> > ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C
> > ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O
> > ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N
> > ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C
> > ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C
> > ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O
> > ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C
> > ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C
> > ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N
> > ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O
> > ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N
> > ATOM 56 CA GLY A 8 9.422 10.75
Re: [PyMOL] counting number of standard amino acids in PDB
Thank you, Jared! how do you think would it be possible to run this command from no-gui pymol? pymol -c -d " from pymol import cmd print len( set( [(i.chain,i.resi,i.resn) for i in cmd.get_model(selection).atom] ) ) " ? пн, 24 июн. 2019 г. в 16:17, Jared Sampson : > > Hi James - > > Do any of the options from this previous BB discussion help? > > https://sourceforge.net/p/pymol/mailman/message/28466955/ > > Cheers, > Jared > > > On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) > wrote: > > Dear Pymol Users, > > that is not very related to pymol question but however probably it can > be solved via pymol as well ;-) > > I am looking for some script (e.g. via running in pymol no-gui), which > will count the number of standard amino acid residues in the given > PDB. E.g. for particular pdb consisted of 9 residues complexed with > part of the ligand I need to print the value of 9 (the end value of > 6th column before TER) > > ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N > ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C > ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C > ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O > ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C > ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C > ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S > ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C > ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N > ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C > ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C > ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O > ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C > ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C > ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C > ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C > ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+ > ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N > ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C > ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C > ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O > ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C > ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C > ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C > ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C > ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C > ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C > ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C > ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N > ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C > ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C > ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O > ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C > ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C > ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O > ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N > ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C > ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C > ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O > ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C > ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C > ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C > ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N > ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C > ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C > ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O > ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N > ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C > ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C > ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O > ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C > ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C > ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N > ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O > ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N > ATOM 56 CA GLY A 8 9.422 10.752 -0.139 1.00 27.40 C > ATOM 57 C GLY A 8 9.309 10.498 -1.629 1.00 27.35 C > ATOM 58 O GLY A 8 8.449 11.071 -2.303 1.00 27.93 O > ATOM 59 N GLN A 9 10.178 9.630 -2.136 1.00 26.80 N > ATOM 60 CA GLN A 9 10.215 9.294 -3.552 1.00 26.37 C > ATOM 61 C GLN A 9 9.834 7.833 -3.736 1.00 25.75 C > ATOM 62 O GLN A 9 10.308 6.970 -2.997 1.00 25.25 O > ATOM 63 CB GLN A 9 11.622 9.522 -4.115 1.00 26.74 C > ATOM 64 CG GLN A 9 12.197 10.924 -3.899 1.00 27.40 C > ATOM 65 CD GLN A 9 11.327 12.028 -4.475 1.00 29.17 C > ATOM 66 NE2 GLN A 9 10.896 11.863 -5.726 1.00 29.46 N > ATOM 67 OE1 GLN A 9 11.048 13.025 -3.800 1.00 31.02 O > TER > ATOM 1719 C1 0XB B 220 6.613 3.931 -16.928 1.00 11.35 C > ATOM 1720 C2 0XB B 220 7.042 5.128 -16.070 1.00 14.60 C > ATOM 1721 O2 0XB B 220 6.3
[PyMOL] counting number of standard amino acids in PDB
Dear Pymol Users, that is not very related to pymol question but however probably it can be solved via pymol as well ;-) I am looking for some script (e.g. via running in pymol no-gui), which will count the number of standard amino acid residues in the given PDB. E.g. for particular pdb consisted of 9 residues complexed with part of the ligand I need to print the value of 9 (the end value of 6th column before TER) ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+ ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N ATOM 56 CA GLY A 8 9.422 10.752 -0.139 1.00 27.40 C ATOM 57 C GLY A 8 9.309 10.498 -1.629 1.00 27.35 C ATOM 58 O GLY A 8 8.449 11.071 -2.303 1.00 27.93
Re: [PyMOL] pymol in no-gui mode
thank you very much, Ali!
I only changed the quotes in your script because I have integrated it
to my shell script in order to use with the varibables:
# run pymol to align the snapshots and save it to the session
pymol -c -d "
from pymol import cmd
cmd.load('${sim}/${simulation}_after_minimization.pdb')
cmd.load('${sim}/${simulation}_after_equilibration.pdb')
cmd.remove('resn WAT')
cmd.super('${simulation}_after_equilibration*','${simulation}_after_minimization*')
cmd.bg_color('white')
cmd.save('${output}/!!!pymol_sessions/${simulation}_superimposed.pse')
"
вс, 23 июн. 2019 г. в 12:05, Ali Kusay :
>
> Hi James,
>
> Just a follow up, I would still recommend you use the script in a file to do
> this as it is less messy but it can be done:
>
> pymol -c -d '
> from pymol import cmd
> cmd.load("A.pdb")
> cmd.load("B.pdb")
> cmd.load("C.pdb")
> cmd.super("C*","A*")
> cmd.super("B*","A*")
> cmd.bg_color("white")
> cmd.save("output.pse")
> '
>
> If you paste the above as is in shell It should work provided you are the
> directory containing the 3 pdb files
>
> Executing pymol with -d flag in shell means you can input pymol commands, to
> get around indentation you can run leave an ' apostrophe at the end to paste
> the scripts in and execute all as a string without needing to save as a file
>
> Just for reference, the -c flag is "batch processing (no GUI)" and the
> commands above can be saved into a python file and ran using:
>
> pymol -c -r "path_to_script"
>
> Hope this helps.
>
> Cheers,
>
> Ali
>
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: akus8...@uni.sydney.edu.au
>
>
> On 23/6/19, 7:00 pm, "James Starlight" wrote:
>
> hello there,
>
> As a part of my scripting routine, I would like to use pymol in no-gui
> mode (directly in the linux shell) to do the following things:
> 1) load in pymol 3 conformations of the same protein, which are
> defined as A.pdb B.pdb C.pdb
> 2) superimpose C to A using "super" or alternatively (which is better)
> "alignall" to A
> 3) change background of the session to white :-)
> 4) save the pymol session for the superimposed A B and C as the *.pse
> output file
>
> could you suggest me 1 string command for pymol, which I can directly
> use in shell terminal to do the mentioned routines in no-gui mode?
>
> thanks you!!
>
> James
>
>
> ___
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[PyMOL] pymol in no-gui mode
hello there, As a part of my scripting routine, I would like to use pymol in no-gui mode (directly in the linux shell) to do the following things: 1) load in pymol 3 conformations of the same protein, which are defined as A.pdb B.pdb C.pdb 2) superimpose C to A using "super" or alternatively (which is better) "alignall" to A 3) change background of the session to white :-) 4) save the pymol session for the superimposed A B and C as the *.pse output file could you suggest me 1 string command for pymol, which I can directly use in shell terminal to do the mentioned routines in no-gui mode? thanks you!! James ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] A structural superimposition and further post-processing
if just add strings in pymol's cmd the "Super version" of the script works fine so the problem is indeed in MAC :) 2017-07-18 20:53 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: > There were some errors in the executing pymol script with your commands using > @ script.pml > or > run script.pml > > probably because of my MAC Pymol which is v 1.74 mb outdated, no? > > BTW on the same MAC I just have tried to install updated setup.py and > it was the following error: > > Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py > File "setup.py", line 7 > > ^ > SyntaxError: invalid syntax > > 2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >> With super instead of tmalign: >> >> loadall *.pdb >> extra_fit *, reference, method=super, object=aln >> remove not (byres aln) >> >> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now: >> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af >> >> Cheers, >> Thomas >> >>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote: >>> >>> Hi Thomas, >>> >>> could you also send the same script but just with the Super command >>> for the superimposition without PSICO? >>> >>> it's strange I have a problems of PSICO installation on MAC with python 3 >>> >>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >>> READMEpsicosetup.py >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >>> File "setup.py", line 10 >>>print 'Warning: could not import version' >>>^ >>> >>> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >>>> Hi Thomas, >>>> >>>> could you also send the same script but just with the Super command >>>> for the superimposition without PSICO? >>>> >>>> it's strange I have a problems of PSICO installation on MAC with python 3 >>>> >>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>>> Type "help", "copyright", "credits" or "license" for more information. >>>>>>> >>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >>>> READMEpsicosetup.py >>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >>>> File "setup.py", line 10 >>>>print 'Warning: could not import version' >>>>^ >>>> SyntaxError: Missing parentheses in call to 'print' >>>> >>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >>>>> Hi Gleb, >>>>> >>>>> If you have PSICO installed (which provides a TMalign wrapper), then this >>>>> script should be sufficient: >>>>> >>>>> loadall *.pdb >>>>> import psico.fitting >>>>> extra_fit *, reference, method=tmalign, object=aln >>>>> remove not (byres aln) >>>>> >>>>> https://pymolwiki.org/index.php/Psico >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Dear Pymol Users! >>>>>> >>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor >>>>>> reference.pdb (it consist of only one GPCR monomer - seven >>>>>> transmbembrane scaffold). >>>>>> >>>>>> I need to write a simple script which will do the following things: >>>>>> >>>>>> 1 - allign (in loop) each structure against reference.pdb using >>>>>> "super" or "TMalign" (is better!) >>>>>> >>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions >>>>>> (assuming that each pdb has several chains, some insertions like >>>>>> lyzocyme which were not aligned against reference), thus keeping only >>>>>> seven-transmembrane scaffold present in reference.pdb. >>>>>> >>>>>> I thanks so much for the help! >>>>>> >>>>>> Gleb >> >> -- >> Thomas Holder >> PyMOL Principal Developer >> Schrödinger, Inc. >> -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A structural superimposition and further post-processing
There were some errors in the executing pymol script with your commands using @ script.pml or run script.pml probably because of my MAC Pymol which is v 1.74 mb outdated, no? BTW on the same MAC I just have tried to install updated setup.py and it was the following error: Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py File "setup.py", line 7 ^ SyntaxError: invalid syntax 2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: > With super instead of tmalign: > > loadall *.pdb > extra_fit *, reference, method=super, object=aln > remove not (byres aln) > > The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now: > https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af > > Cheers, > Thomas > >> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote: >> >> Hi Thomas, >> >> could you also send the same script but just with the Super command >> for the superimposition without PSICO? >> >> it's strange I have a problems of PSICO installation on MAC with python 3 >> >> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >> Type "help", "copyright", "credits" or "license" for more information. >>>>> >> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >> READMEpsicosetup.py >> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >> File "setup.py", line 10 >>print 'Warning: could not import version' >>^ >> >> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >>> Hi Thomas, >>> >>> could you also send the same script but just with the Super command >>> for the superimposition without PSICO? >>> >>> it's strange I have a problems of PSICO installation on MAC with python 3 >>> >>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t >>> READMEpsicosetup.py >>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py >>> File "setup.py", line 10 >>>print 'Warning: could not import version' >>>^ >>> SyntaxError: Missing parentheses in call to 'print' >>> >>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >>>> Hi Gleb, >>>> >>>> If you have PSICO installed (which provides a TMalign wrapper), then this >>>> script should be sufficient: >>>> >>>> loadall *.pdb >>>> import psico.fitting >>>> extra_fit *, reference, method=tmalign, object=aln >>>> remove not (byres aln) >>>> >>>> https://pymolwiki.org/index.php/Psico >>>> >>>> Cheers, >>>> Thomas >>>> >>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> >>>>> wrote: >>>>> >>>>> Dear Pymol Users! >>>>> >>>>> In my work dir I have 200 pdb files of GPCRs and one receptor >>>>> reference.pdb (it consist of only one GPCR monomer - seven >>>>> transmbembrane scaffold). >>>>> >>>>> I need to write a simple script which will do the following things: >>>>> >>>>> 1 - allign (in loop) each structure against reference.pdb using >>>>> "super" or "TMalign" (is better!) >>>>> >>>>> 2 - from each of the aligned pdbs, remove not superimposed regions >>>>> (assuming that each pdb has several chains, some insertions like >>>>> lyzocyme which were not aligned against reference), thus keeping only >>>>> seven-transmembrane scaffold present in reference.pdb. >>>>> >>>>> I thanks so much for the help! >>>>> >>>>> Gleb > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A structural superimposition and further post-processing
Hi Thomas,
could you also send the same script but just with the Super command
for the superimposition without PSICO?
it's strange I have a problems of PSICO installation on MAC with python 3
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
READMEpsicosetup.py
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
File "setup.py", line 10
print 'Warning: could not import version'
^
2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Hi Thomas,
>
> could you also send the same script but just with the Super command
> for the superimposition without PSICO?
>
> it's strange I have a problems of PSICO installation on MAC with python 3
>
> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>>
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
> READMEpsicosetup.py
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
> File "setup.py", line 10
> print 'Warning: could not import version'
> ^
> SyntaxError: Missing parentheses in call to 'print'
>
> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>> Hi Gleb,
>>
>> If you have PSICO installed (which provides a TMalign wrapper), then this
>> script should be sufficient:
>>
>> loadall *.pdb
>> import psico.fitting
>> extra_fit *, reference, method=tmalign, object=aln
>> remove not (byres aln)
>>
>> https://pymolwiki.org/index.php/Psico
>>
>> Cheers,
>> Thomas
>>
>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com>
>>> wrote:
>>>
>>> Dear Pymol Users!
>>>
>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>> reference.pdb (it consist of only one GPCR monomer - seven
>>> transmbembrane scaffold).
>>>
>>> I need to write a simple script which will do the following things:
>>>
>>> 1 - allign (in loop) each structure against reference.pdb using
>>> "super" or "TMalign" (is better!)
>>>
>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>> (assuming that each pdb has several chains, some insertions like
>>> lyzocyme which were not aligned against reference), thus keeping only
>>> seven-transmembrane scaffold present in reference.pdb.
>>>
>>> I thanks so much for the help!
>>>
>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
--
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[PyMOL] A structural superimposition and further post-processing
Dear Pymol Users! In my work dir I have 200 pdb files of GPCRs and one receptor reference.pdb (it consist of only one GPCR monomer - seven transmbembrane scaffold). I need to write a simple script which will do the following things: 1 - allign (in loop) each structure against reference.pdb using "super" or "TMalign" (is better!) 2 - from each of the aligned pdbs, remove not superimposed regions (assuming that each pdb has several chains, some insertions like lyzocyme which were not aligned against reference), thus keeping only seven-transmembrane scaffold present in reference.pdb. I thanks so much for the help! Gleb -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Coordination bonds
Dear PyMol users! Using present -> ligand sites context menu I would like to display possible non-covalent contacts between ions embedded within the protein. First I tried to rename ATOM to HETATM record corresponds to ions however pymol still don't recognize ions as ligand. Will be very thankful for any suggestions! James -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Scripting in Pymol (+)
Dear Pymol Users! Here I desice to continue my topic regarding scripting in Pymol; My current task: I have 1 X-ray structure of cythochrome-C with HEME residue embedded within the protein as a cofactor I have 10 snapshots of cythochrome-C from MD trajectory where HEME was not present explicitly What I need from pymol to write some script, which will 1) align (superimpose) each MD snapshot againt reference 2) copy HEME residue from reference to each of the superimpsoed snapshot within the same position. Thanks so much for any suggestions regarding realization ! James -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Transfer of the selection from reference to the ensemble
Dear Pymol Users! Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with cofactors (ligand and metals); 2) ensemble of 20 md snapshots of the same proteins superimposed on each others without any cofactors; For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs). I will be very thankful for any suggestions for practical realization of those steps! James -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Analysis of docking poses from 2 nmr-ensembles
Dear Pymol users! I am studying protein-protein assosiation using 2 different proteins as test case by means of variety of computational methods. For my particular caseI need to compare binding poses emerged as the result of protein-protein docking (ensemble 1: which consists of 20 snapshots according to docking ranking) as well as MD simulation (ensemble 2: which consists of 10 snapshots each of which represents binding pose which has been established during long MD run). Loading those two ensembles in pymol as 2 different models (in NMR-like model format) I need to performs some analysis to find some shared trends in each of them e.g RMSD of the distances between common residues-pairs found in contact map analysis or something else. What are most trivial suggestions might be in that particular case? Thanks for the suggestions! James -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] post-processing of pdb ensemble
More precisely I would like to know how to script in pymol the following alteration fo the chains for the multi-chain pdb PyMOL>alter (bound_combined and chain B), chain="A" Alter: modified 5157 atoms. PyMOL>alter (bound_combined and chain C), chain="B" Alter: modified 2285 atoms. PyMOL>alter (bound_combined and chain D), chain="C" Alter: modified 2778 atoms. PyMOL>alter (bound_combined and chain E), chain="D" Alter: modified 1560 atoms. PyMOL>alter (bound_combined and chain F), chain="E" Alter: modified 1114 atoms. PyMOL>alter (bound_combined and chain G), chain="F" Alter: modified 950 atoms. PyMOL>alter (bound_combined and chain H), chain="G" Alter: modified 895 atoms. PyMOL>alter (bound_combined and chain I), chain="H" Alter: modified 843 atoms. PyMOL>alter (bound_combined and chain J), chain="I" Alter: modified 806 atoms. PyMOL>alter (bound_combined and chain K), chain="J" Alter: modified 574 atoms. PyMOL>alter (bound_combined and chain L), chain="K" Alter: modified 501 atoms. PyMOL>alter (bound_combined and chain M), chain="L" Alter: modified 511 atoms. PyMOL>alter (bound_combined and chain N), chain="M" Alter: modified 433 atoms. So each step we rename chain i to the i-1 name within given model :) Thanks! J. 2016-05-23 19:11 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: > Dear Pymol users! > > After some post-processing of MD simulation I have extracted from the > traejctory several snapshots as individual pdbs which I need to > 1- to re-assign information regarding chain letters (which was lost > after some operations on pdbs) for all of those structures assuming > that within each of these pdbs residues are ordered correctly e.g from > (1-104 which > should be chain A) than from 1-100 (it should be chain B), than 1-70 > (in should be chain C) etc. > > 2- superimpose and combine all of the pdbs within one model in nmr-like > format. > > Thanks for help! > > James -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] post-processing of pdb ensemble
Dear Pymol users! After some post-processing of MD simulation I have extracted from the traejctory several snapshots as individual pdbs which I need to 1- to re-assign information regarding chain letters (which was lost after some operations on pdbs) for all of those structures assuming that within each of these pdbs residues are ordered correctly e.g from (1-104 which should be chain A) than from 1-100 (it should be chain B), than 1-70 (in should be chain C) etc. 2- superimpose and combine all of the pdbs within one model in nmr-like format. Thanks for help! James -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Contact map visualizer
Thanks Tsjerk! now the map is accepted fine by the Pymol- however there is an problem due to the mismatching of atoms in ref structure and the map (although I use ref.pdf from which contact map has been produced). Probably the source of the error is Martini's atom representation used in my system - I've had the same issue in case of some VMD script which do the same task. Do any alternativeties are exist which can identify residues (even on one of the protein) crucial for the formation of the complex during md run with the possibility to map it to the structure for the visualization? J. 2016-05-12 12:52 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>: > Hey :) > > That's been a choice of the author. You can contact him and ask. > > Cheers, > > Tsjerk > > On May 12, 2016 12:25, "James Starlight" <jmsstarli...@gmail.com> wrote: >> >> Ok, thanks! >> >> however it's normal that pymol ask me for the contact map in the png >> and not for the original xpm produced by gromacs? It seems for the >> that to operate directly with Pymol outputs is more trivial :-) >> >> J. >> >> 2016-05-12 6:51 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>: >> > Hi James, >> > >> > You can convert the .xpm file to .png/.jpg using tools like convert >> > (imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm >> > right, >> > but it's an easy one to try. >> > >> > Cheers, >> > >> > Tsjerk >> > >> > On May 11, 2016 2:40 PM, "James Starlight" <jmsstarli...@gmail.com> >> > wrote: >> >> >> >> Dear Pymol users! >> >> >> >> I am in charge with the analysis of protein-protein association during >> >> long molecular dynamic simulation. In particularly I am interesting to >> >> find residues on one of the protein which are crustal for the binding >> >> interface established during Md. >> >> For that purpose I am trying to use Contact map visualizer plugin to >> >> map contact maps produced by gromacs onto the 3D structure via Pymol. >> >> The problem that on the stage of loading of the contact map Pymol >> >> proposed me to load only png or jpg files (not xpm produced by >> >> g_mdmat). How it's possible to solve the issue? Any other suggestions >> >> regarding my topic? >> >> >> >> Thanks! >> >> >> >> James >> >> >> >> >> >> >> >> -- >> >> Mobile security can be enabling, not merely restricting. Employees who >> >> bring their own devices (BYOD) to work are irked by the imposition of >> >> MDM >> >> restrictions. Mobile Device Manager Plus allows you to control only the >> >> apps on BYO-devices by containerizing them, leaving personal data >> >> untouched! >> >> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j >> >> ___ >> >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Contact map visualizer
Dear Pymol users! I am in charge with the analysis of protein-protein association during long molecular dynamic simulation. In particularly I am interesting to find residues on one of the protein which are crustal for the binding interface established during Md. For that purpose I am trying to use Contact map visualizer plugin to map contact maps produced by gromacs onto the 3D structure via Pymol. The problem that on the stage of loading of the contact map Pymol proposed me to load only png or jpg files (not xpm produced by g_mdmat). How it's possible to solve the issue? Any other suggestions regarding my topic? Thanks! James -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Bash scripting and pymol
Yes thanks it works!
Now assuming that I want to make alitle complicated script based on
that template.
Assuming that I have 3 pdbs used as references defined in variables
ref1, ref2,ref3
now I need loop all of my pdbs from the array and superimpose each pdb
from the array agains each of reference pdb and then based on RMSD
value produced from pymol output chose only best superimposed
structure from 3 possibilities
Based on that selection I can make conclusion that for pdb1 the ref1
is best template because of the similar fold, for pdb2 is the ref2 is
best etc...
# Set pdb array
pdb_array=("1f88" "2rh1" "3pbs" "3eml" "4LGJ" "5A2H")
pdb_array_store=$template/pymol
# Set references
ref1="${pdb_array_store}/ref/ref_gpcr.pdb"
ref1_filename=$(basename "$ref1")
R1=${ref1_filename/.pdb/}
ref2="${pdb_array_store}/ref/ref_wsp.pdb"
ref2_filename=$(basename "$ref2")
R2=${ref2_filename/.pdb/}
ref3="${pdb_array_store}/ref/ref_xz.pdb"
ref3_filename=$(basename "$ref3")
R3=${ref3_filename/.pdb/}
Here the realization of that for only 1 reference:
# download pdbs to the folder and superimpose them agains ref1!
for i in ${pdb_array[@]}; do
pdb_tit=$(basename "$i")
pymol ${ref1} -d "cd ${pdb_array_store}/tmp; fetch ${i}, async=0;
remove ${i} and not chain A; super ${i}, ${R1}; save
${pdb_array_store}/${pdb_tit}_superimposed.pdb, ${pdb_tit} and
polymer;" -c #> ${pdb_array_store}/tmp/${pdb_tit}_pymol.log
done
now I can just define ref2 ref3 and add two additional pymol strings
within the for loop to superimpose step-by-stem each pdbs from the
${pdb_array} agains, ref2 and ref3 in addition.
but how to select the best superimposed structure as the outcome of
each for loop run ? In other words I need only to save
${pdb_tit}_superimposed.pdb with the lowest RMSD value assuming that
the operation was repeated 3 times for 3 different refs.
Thanks for help!
J,
2016-04-28 15:48 GMT+02:00 David Hall <li...@cowsandmilk.net>:
> You need to add “,async=0” to your fetch calls.
>
> http://pymolwiki.org/index.php/Fetch
>
>
>
>> On Apr 28, 2016, at 4:51 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> Hi,
>>
>> My script is
>>
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> pdb_array_store=$template/pymol
>>
>>
>> # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process
>> them!
>> mkdir ${pdb_array_store}
>> for i in ${pdb_array[@]}; do
>> pdb_tit=$(basename "$i")
>> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
>> ${pdb_tit}" -c ;
>> rm ${pdb_array_store}/*.log
>> done
>>
>>
>> while executing it sends error
>>
>> PyMOL>fetch 5A2H; save
>> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
>> 5A2H
>> please wait ...
>> Selector-Error: Invalid selection name "5A2H".
>> ( 5A2H )<--
>> Save: wrote
>> "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
>> PyMOL: normal program termination.
>>
>> if I change save selection just to 'polymer' it saved empty pdbs-
>> where might be an error here?
>>
>> Thanks!
>>
>> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>>> Hi,
>>>
>>> You need
>>>
>>> for i in ${pdb_array[@]}
>>> do
>>> ...
>>> done
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
>>>>
>>>> so As I tried to do it but it was not worked :-O)
>>>>
>>>> #pdbs list
>>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>>> #where to save
>>>> pdb_array_store=$template/pymol/
>>>>
>>>>
>>>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>>>> #mkdir ${pdb_array_store}
>>>> for i in `cat ${pdb_array}` ; do wget
>>>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>>>> done
>>>>
>>>> result
>>>> cat: 1UBI: No such file or directory
>>>>
>>>> 2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>>>>> Please give me an example of the list of 3 pdbs instead of just cat $1
>>>>> :)
>>>>> as well as proper
Re: [PyMOL] Bash scripting and pymol
Hi,
My script is
pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
pdb_array_store=$template/pymol
# A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them!
mkdir ${pdb_array_store}
for i in ${pdb_array[@]}; do
pdb_tit=$(basename "$i")
pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
${pdb_tit}" -c ;
rm ${pdb_array_store}/*.log
done
while executing it sends error
PyMOL>fetch 5A2H; save
/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
5A2H
please wait ...
Selector-Error: Invalid selection name "5A2H".
( 5A2H )<--
Save: wrote
"/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
PyMOL: normal program termination.
if I change save selection just to 'polymer' it saved empty pdbs-
where might be an error here?
Thanks!
2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hi,
>
> You need
>
> for i in ${pdb_array[@]}
> do
> ...
> done
>
> Cheers,
>
> Tsjerk
>
> On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
>>
>> so As I tried to do it but it was not worked :-O)
>>
>> #pdbs list
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> #where to save
>> pdb_array_store=$template/pymol/
>>
>>
>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>> #mkdir ${pdb_array_store}
>> for i in `cat ${pdb_array}` ; do wget
>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>> done
>>
>> result
>> cat: 1UBI: No such file or directory
>>
>> 2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> > Please give me an example of the list of 3 pdbs instead of just cat $1
>> > :)
>> > as well as proper syntax of how to save each pdb after fetching in
>> > pymol using same command line
>> > Forgot to mention important points:
>> > 1) that list should be physically in my script like in python
>> > 2) I use pymol because I will need to process each of the pdb- e,g to
>> > remove from them ligands or water etc
>> >
>> > Thanks!
>> >
>> > 2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> >> Please give me an example of the list of 3 pdbs instead of cat $1 as
>> >> well as how to save syntax of how to save each pdb
>> >>
>> >>
>> >> Thanks!
>> >>
>> >> J
>> >>
>> >> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>> >>> If you really want to use pymol, this works
>> >>>
>> >>> #!/bin/bash
>> >>> #myscript.bash
>> >>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>> >>>
>> >>>
>> >>> Then on the command line
>> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>> >>>
>> >>>
>> >>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com>
>> >>> wrote:
>> >>>
>> >>> Must you use pymol?
>> >>>
>> >>>
>> >>> Try directly from the PDB
>> >>>
>> >>> #!/bin/bash
>> >>> #myscript.bash
>> >>>
>> >>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
>> >>> done
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Then on the command line
>> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>> >>>
>> >>>
>> >>> J
>> >>>
>> >>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com>
>> >>> wrote:
>> >>>
>> >>> Dear Pymol users!
>> >>>
>> >>> I need to add a few strings to my simple bash script which will creat
>> >>> a list of pdb files and than will call pymol without GUI from the
>> >>> terminal to fetch all the pdbs and save it to the desired location.
>> >>> For one pdb it should be smth like
>> >>>
>> >>> pdbs="1f88"
>> >>>
>> >>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> >>> ${tmp}/pymol_${pdbs}.log
>>
Re: [PyMOL] Bash scripting and pymol
so As I tried to do it but it was not worked :-O)
#pdbs list
pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
#where to save
pdb_array_store=$template/pymol/
# A simple FETCHER: download pdbs to the folder and pre-process them!
#mkdir ${pdb_array_store}
for i in `cat ${pdb_array}` ; do wget
http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
done
result
cat: 1UBI: No such file or directory
2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Please give me an example of the list of 3 pdbs instead of just cat $1 :)
> as well as proper syntax of how to save each pdb after fetching in
> pymol using same command line
> Forgot to mention important points:
> 1) that list should be physically in my script like in python
> 2) I use pymol because I will need to process each of the pdb- e,g to
> remove from them ligands or water etc
>
> Thanks!
>
> 2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> Please give me an example of the list of 3 pdbs instead of cat $1 as
>> well as how to save syntax of how to save each pdb
>>
>>
>> Thanks!
>>
>> J
>>
>> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>>> If you really want to use pymol, this works
>>>
>>> #!/bin/bash
>>> #myscript.bash
>>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>>>
>>>
>>> Then on the command line
>>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>>
>>>
>>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com> wrote:
>>>
>>> Must you use pymol?
>>>
>>>
>>> Try directly from the PDB
>>>
>>> #!/bin/bash
>>> #myscript.bash
>>>
>>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
>>>
>>>
>>>
>>>
>>> Then on the command line
>>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>>
>>>
>>> J
>>>
>>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>>
>>> Dear Pymol users!
>>>
>>> I need to add a few strings to my simple bash script which will creat
>>> a list of pdb files and than will call pymol without GUI from the
>>> terminal to fetch all the pdbs and save it to the desired location.
>>> For one pdb it should be smth like
>>>
>>> pdbs="1f88"
>>>
>>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>>> ${tmp}/pymol_${pdbs}.log
>>>
>>> will be thankful for the correction of this string as well as example
>>> how it can be adapted for a list of pdbs in bash.
>>>
>>> Thanks!
>>>
>>> J
>>>
>>> --
>>> Find and fix application performance issues faster with Applications Manager
>>> Applications Manager provides deep performance insights into multiple tiers
>>> of
>>> your business applications. It resolves application problems quickly and
>>> reduces your MTTR. Get your free trial!
>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>>
>>>
--
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Re: [PyMOL] Bash scripting and pymol
Please give me an example of the list of 3 pdbs instead of just cat $1 :)
as well as proper syntax of how to save each pdb after fetching in
pymol using same command line
Forgot to mention important points:
1) that list should be physically in my script like in python
2) I use pymol because I will need to process each of the pdb- e,g to
remove from them ligands or water etc
Thanks!
2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Please give me an example of the list of 3 pdbs instead of cat $1 as
> well as how to save syntax of how to save each pdb
>
>
> Thanks!
>
> J
>
> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>> If you really want to use pymol, this works
>>
>> #!/bin/bash
>> #myscript.bash
>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com> wrote:
>>
>> Must you use pymol?
>>
>>
>> Try directly from the PDB
>>
>> #!/bin/bash
>> #myscript.bash
>>
>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
>>
>>
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> J
>>
>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> Dear Pymol users!
>>
>> I need to add a few strings to my simple bash script which will creat
>> a list of pdb files and than will call pymol without GUI from the
>> terminal to fetch all the pdbs and save it to the desired location.
>> For one pdb it should be smth like
>>
>> pdbs="1f88"
>>
>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> ${tmp}/pymol_${pdbs}.log
>>
>> will be thankful for the correction of this string as well as example
>> how it can be adapted for a list of pdbs in bash.
>>
>> Thanks!
>>
>> J
>>
>> --
>> Find and fix application performance issues faster with Applications Manager
>> Applications Manager provides deep performance insights into multiple tiers
>> of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>>
--
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[PyMOL] Bash scripting and pymol
Dear Pymol users!
I need to add a few strings to my simple bash script which will creat
a list of pdb files and than will call pymol without GUI from the
terminal to fetch all the pdbs and save it to the desired location.
For one pdb it should be smth like
pdbs="1f88"
pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
${tmp}/pymol_${pdbs}.log
will be thankful for the correction of this string as well as example
how it can be adapted for a list of pdbs in bash.
Thanks!
J
--
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reduces your MTTR. Get your free trial!
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Re: [PyMOL] Cartoon visualization of per-residue txt data
Hi Tsjerk, the interesting option for coloring which I found to set sensitivity of the visualization in my case: spectrum b, red_orange_white, minimum=-1, maximum=0.1 are there any same commands to set transparency level according to the B-factor value? Here the issue is with the proper selection E.g PyMOLselect not-relevent, b 0 results only in small atoms selected and PyMOLselect ss, b = 0 Selector-Error: Invalid selection. b-- Regards, James 2015-04-10 21:12 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, The selection keyword 'b' exists for just that purpose: to make selections based on the b-factor value. color red, b 0 Cheers, Tsjerk On Fri, Apr 10, 2015 at 5:19 PM, James Starlight jmsstarli...@gmail.com wrote: some specification regarding B-factors visualization for my task: is it possible within the open pymol session 1) to select only residues with non-zero B-factors as specified selection (here I would like to present it as the stics and display it names as the label) 2) to define residues with zero B-factors as another specified selection (for those one I'd like to apply specified color filter for instance and transparency as for not relevant in my case) Thanks! J 2015-04-10 15:27 GMT+02:00 James Starlight jmsstarli...@gmail.com: Hi Osvaldo and thank you very much- it works perfect! The only question which I have- is it possible to modify existing color-pattern of the B-factor colouring (from the spectrum visualization)? for instance I need to colour by white all residues with 0.0 B-factors and as the rainbow from cold to hot gradient residues with non-zero B-factors: where residues with most negative values should correspond to the hot colours, and with positive - to cold (because here this valus in fact correspond to the binding free energy so more negative- better contribution to dG). Thanks again, James 2015-04-10 14:44 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com: Hi James, cmd.alter() is not working because you forget the to add the . You can use PyMol as a regular Python library, write an script and then run it, from the command line, as: python my_script.py Your script should looks like the following: import __main__ __main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI import pymol from pymol import cmd, stored pymol.finish_launching() import other_useful_library cmd.load(OR5P3_androstenone.pdb) # open the file of new values (just 1 column of numbers, one for each alpha carbon) inFile = open(OR5P3_androstenone.dat, 'r') # create the global, stored array newB = [] # read the new B factors from file for line in inFile.readlines(): newB.append( float(line) ) # close the input file inFile.close() # clear out the old B Factors cmd.alter(OR5P3_androstenone, b=0.0) # update the B Factors with new properties cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0)) # color the protein based on the new B Factors of the alpha carbons cmd.spectrum(b, OR5P3_androstenone and n. CA) # save new pdb cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone) Cheers, Osvaldo. On Fri, Apr 10, 2015 at 9:03 AM, James Starlight jmsstarli...@gmail.com wrote: so to be more precise the issue is how to adapt the following script (which used python interpetator directly from pymol to change B-factors within loaded pdb) to use it as the external script loaded from command line e.g pymol -r script.py # here the code what should I to adapt: cmd.load(OR5P3_androstenone.pdb) # open the file of new values (just 1 column of numbers, one for each alpha carbon) inFile = open(OR5P3_androstenone.dat, 'r') # create the global, stored array newB = [] # read the new B factors from file for line in inFile.readlines(): newB.append( float(line) ) # close the input file inFile.close() # clear out the old B Factors cmd.alter(OR5P3_androstenone, b=0.0) # update the B Factors with new properties cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0)) # color the protein based on the new B Factors of the alpha carbons cmd.spectrum(b, OR5P3_androstenone and n. CA) # save new pdb cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone) # so as you can see here I tried to move some pynol command like alter to the cmd.alter with its options but the script didn't worked. J. 2015-04-09 16:52 GMT+02:00 James Starlight jmsstarli...@gmail.com: also to specify: I've already done this for one pdb and one dat file using just sequence command from the pymol with loaded protA.pdb inFile = open(./test.dat, 'r') # create the global, stored array stored.newB = [] # read the new B factors from file for line in inFile.readlines(): stored.newB.append( float(line) ) # close the input file inFile.close
Re: [PyMOL] Pymol molecular visualisation
Thanks ! still have not found solution for grid-mode display: 1- I need to show names of each opened object near its cartoon 2- I need to increase spacing of grid border (m.b like just empty space)- to better discriminate between opened objects in case of its high zooming J 2015-04-11 14:51 GMT+02:00 João M. Damas jmda...@itqb.unl.pt: 1- See http://www.pymolwiki.org/index.php/Ray_Trace_Gain. However, from my experience, I don't think the setting works too well, so what I usually do is to increase the resolution of the raytrace, which makes the black outline thinner. On Fri, Apr 10, 2015 at 4:48 PM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! Here I will ask some question regarding visualization issues in pymol. 1- Using ray_trace_mode, 1 I need to decrease at least twisty width of black countour line (especially in the loop segments). 2- Being in the split mode (visualization of the several objects on one screen) I need to show title of each of the objects somewhere near of its cartoon area (e,g in right upper corner)- just to know on the produced picture names of the corresponded cartoon. 3- Also please have a look on my another topic regarding visualization of B-factor gradients: actually I need to revert its existing color pattern and select residues according to it's actual B-factor values (E.g with B-factor=0, with negative and/or positive) for its subsequent selective visualization. Thanks a lot for the advises! -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Cartoon visualization of per-residue txt data
and also a question- how it would be possible to do something with the selection based on the b-factors e.g PyMOLselect ss, b -0.2 Selector: selection ss defined with 119 atoms. than I've tried to make visualization of the residues within the ss to display residues names from the label context menu, which resulted in the Selector-Error: Misplaced ). Selector-Error: Malformed selection. ( ss )-- Selector-Error: Misplaced ). Selector-Error: Malformed selection. also I've tried just to copy 'ss' to new object: ( ( name CA+C1*+C1' and ( byres ( ss )-- Selector-Error: Misplaced ). Selector-Error: Malformed selection. ( ss )-- James 2015-04-12 15:12 GMT+02:00 James Starlight jmsstarli...@gmail.com: Hi Tsjerk, the interesting option for coloring which I found to set sensitivity of the visualization in my case: spectrum b, red_orange_white, minimum=-1, maximum=0.1 are there any same commands to set transparency level according to the B-factor value? Here the issue is with the proper selection E.g PyMOLselect not-relevent, b 0 results only in small atoms selected and PyMOLselect ss, b = 0 Selector-Error: Invalid selection. b-- Regards, James 2015-04-10 21:12 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, The selection keyword 'b' exists for just that purpose: to make selections based on the b-factor value. color red, b 0 Cheers, Tsjerk On Fri, Apr 10, 2015 at 5:19 PM, James Starlight jmsstarli...@gmail.com wrote: some specification regarding B-factors visualization for my task: is it possible within the open pymol session 1) to select only residues with non-zero B-factors as specified selection (here I would like to present it as the stics and display it names as the label) 2) to define residues with zero B-factors as another specified selection (for those one I'd like to apply specified color filter for instance and transparency as for not relevant in my case) Thanks! J 2015-04-10 15:27 GMT+02:00 James Starlight jmsstarli...@gmail.com: Hi Osvaldo and thank you very much- it works perfect! The only question which I have- is it possible to modify existing color-pattern of the B-factor colouring (from the spectrum visualization)? for instance I need to colour by white all residues with 0.0 B-factors and as the rainbow from cold to hot gradient residues with non-zero B-factors: where residues with most negative values should correspond to the hot colours, and with positive - to cold (because here this valus in fact correspond to the binding free energy so more negative- better contribution to dG). Thanks again, James 2015-04-10 14:44 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com: Hi James, cmd.alter() is not working because you forget the to add the . You can use PyMol as a regular Python library, write an script and then run it, from the command line, as: python my_script.py Your script should looks like the following: import __main__ __main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI import pymol from pymol import cmd, stored pymol.finish_launching() import other_useful_library cmd.load(OR5P3_androstenone.pdb) # open the file of new values (just 1 column of numbers, one for each alpha carbon) inFile = open(OR5P3_androstenone.dat, 'r') # create the global, stored array newB = [] # read the new B factors from file for line in inFile.readlines(): newB.append( float(line) ) # close the input file inFile.close() # clear out the old B Factors cmd.alter(OR5P3_androstenone, b=0.0) # update the B Factors with new properties cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0)) # color the protein based on the new B Factors of the alpha carbons cmd.spectrum(b, OR5P3_androstenone and n. CA) # save new pdb cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone) Cheers, Osvaldo. On Fri, Apr 10, 2015 at 9:03 AM, James Starlight jmsstarli...@gmail.com wrote: so to be more precise the issue is how to adapt the following script (which used python interpetator directly from pymol to change B-factors within loaded pdb) to use it as the external script loaded from command line e.g pymol -r script.py # here the code what should I to adapt: cmd.load(OR5P3_androstenone.pdb) # open the file of new values (just 1 column of numbers, one for each alpha carbon) inFile = open(OR5P3_androstenone.dat, 'r') # create the global, stored array newB = [] # read the new B factors from file for line in inFile.readlines(): newB.append( float(line) ) # close the input file inFile.close() # clear out the old B Factors cmd.alter(OR5P3_androstenone, b=0.0) # update the B Factors with new properties cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0)) # color the protein based on the new B Factors of the alpha carbons cmd.spectrum(b, OR5P3_androstenone
Re: [PyMOL] Cartoon visualization of per-residue txt data
thanks for the information! Here I ask to provide me with some more help because I'm not a big expert in the python . For instance I have 2 folders- one with 10 pdb's corresponded to the 10 complexes of one receptor (289 residues) docked with 10 different ligands; the second one is the 10 the_same_name.dat files corresponded to the 10 logs having 1 column with the values per each residue (totally 289 values) of the receptor. I need to associate each pdb with each dat to exchange existing B-factors within each pdb onto the values taken from the corresponded.dat files and associate it's directly to the C-alpha atoms of each complex for instance. Will it be better to rewrite here the script from the PyMol Wiki or to use data2bfactor.py (here as I found I need to modify my dat logs including to them number of receptor residues and chainID). James 2015-04-08 19:00 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com: Hi James, I think what you want to do is to load your data to the b-factor column of the pdb file and then ask PyMol to color the protein according to the b-factor values. Try with this example from the PyMol wiki and let us know if you find some trouble. Regards, Osvaldo. On Wed, Apr 8, 2015 at 1:47 PM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! For better visualization of the MMGBSA outputs from MD performed for 10 ligands agains 1 receptor-target I wonder to map per-residue decomposition data from each of the systems onto the receptor's 3D structure. Eventually I'd like to produce 10 cartoon diagrams which would differs in the coloring according to the difference in the contribution of residues from the receptor's cavity to binding for different ligands. I will be very thankful if someone provide me with ideas of how such visualization could be done using receptors structure, decomposition logs as the inputs and/or pymol. Here some general idea whig came in mind- import column from the mmgbsa.log directly (with number of rows= number of receptors residues) to the receptor.pdb B-factors column (for instance making meaningful value for C-alpha atom and 0 for the rest). Will be very thankful for some examples of how it could be achieved e.g using combination of awk_sed if more trivial way is not exist. Thanks for help!! James -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Cartoon visualization of per-residue txt data
also to specify:
I've already done this for one pdb and one dat file using just
sequence command from the pymol with loaded protA.pdb
inFile = open(./test.dat, 'r')
# create the global, stored array
stored.newB = []
# read the new B factors from file
for line in inFile.readlines(): stored.newB.append( float(line) )
# close the input file
inFile.close()
# clear out the old B Factors
alter protA, b=0.0
# update the B Factors with new properties
alter protA and n. CA, b=stored.newB.pop(0)
# color the protein based on the new B Factors of the alpha carbons
cmd.spectrum(b, protA and n. CA)
now the idea using below bash script which superimpose each pdb with
each log to call pymol from the terminal each time for each pdb and
load to it corresponded dat file producing as the result new pdb with
new B-factors (taken from the dat log)
#!/bin/bash
workdir=/data2/Gleb/script/Simulations/activation/5p3_decomposition_visu
pdb_all=${workdir}/complexes
logs_all=${workdir}/logs
# where final pdb will be saved
output=${workdir}/outputs
#looping of pdbs
for pdb in ${pdb_all}/*.pdb; do #
pdb_n_full=$(basename ${pdb})
pdb_n=${pdb_n_full%.*}
Complexes=(${Complexes[@]} ${pdb_n});
echo ${pdb_n} has been added to the list!
done
#sort elements within ${Complexes[@]} lists!!
#echo The pdb list consist of: ${Complexes[@]}
#echo Total number of pdbs: ${#Complexes[@]}
#looping of tops
for log in ${logs_all}/*.dat; do #
log_n_full=$(basename ${log})
log_n=${log_n_full%.*}
Logs=(${Logs[@]} ${log_n});
echo ${log_n} has been added to the list!
done
#sort elements within ${Logs[@] lists!!
#echo The DAT list consist of: ${Logs[@]}
#echo Total number of logs: ${#Logs[@]}
# So I need only to define how I will use pymol with each pair of log and pdb
#proceed each pdb in pymol using elements from both lists
for i in $(seq 1 ${#Logs[@]}); do
# print what pdb and what DAT will be used within this loop
echo ${Logs[i]}
echo ${Complexes[i]}
# here run pymol using i pdb with corresponded i dat !!
#done
I will be thankful for any ideas in the last part of that script!
James
2015-04-09 16:15 GMT+02:00 James Starlight jmsstarli...@gmail.com:
thanks for the information! Here I ask to provide me with some more
help because I'm not a big expert in the python .
For instance I have 2 folders- one with 10 pdb's corresponded to the
10 complexes of one receptor (289 residues) docked with 10 different
ligands; the second one is the 10 the_same_name.dat files corresponded
to the 10 logs having 1 column with the values per each residue
(totally 289 values) of the receptor. I need to associate each pdb
with each dat to exchange existing B-factors within each pdb onto the
values taken from the corresponded.dat files and associate it's
directly to the C-alpha atoms of each complex for instance. Will it be
better to rewrite here the script from the PyMol Wiki or to use
data2bfactor.py (here as I found I need to modify my dat logs
including to them number of receptor residues and chainID).
James
2015-04-08 19:00 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com:
Hi James,
I think what you want to do is to load your data to the b-factor column of
the pdb file and then ask PyMol to color the protein according to the
b-factor values. Try with this example from the PyMol wiki and let us know
if you find some trouble.
Regards,
Osvaldo.
On Wed, Apr 8, 2015 at 1:47 PM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Pymol users!
For better visualization of the MMGBSA outputs from MD performed for 10
ligands
agains 1 receptor-target I wonder to map per-residue decomposition
data from each of the systems onto the receptor's 3D structure.
Eventually I'd like to produce 10 cartoon diagrams which would differs
in the coloring according to the difference in the contribution of
residues from the receptor's cavity to binding for different ligands.
I will be very thankful if someone provide me with ideas of how such
visualization could be done using receptors structure, decomposition
logs as the inputs and/or pymol. Here some general idea whig came in
mind- import column from the mmgbsa.log directly (with number of
rows= number of receptors residues) to the receptor.pdb B-factors
column (for instance making meaningful value for C-alpha atom and 0
for the rest). Will be very thankful for some examples of how it could
be achieved e.g using combination of awk_sed if more trivial way is
not exist.
Thanks for help!!
James
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[PyMOL] Cartoon visualization of per-residue txt data
Dear Pymol users! For better visualization of the MMGBSA outputs from MD performed for 10 ligands agains 1 receptor-target I wonder to map per-residue decomposition data from each of the systems onto the receptor's 3D structure. Eventually I'd like to produce 10 cartoon diagrams which would differs in the coloring according to the difference in the contribution of residues from the receptor's cavity to binding for different ligands. I will be very thankful if someone provide me with ideas of how such visualization could be done using receptors structure, decomposition logs as the inputs and/or pymol. Here some general idea whig came in mind- import column from the mmgbsa.log directly (with number of rows= number of receptors residues) to the receptor.pdb B-factors column (for instance making meaningful value for C-alpha atom and 0 for the rest). Will be very thankful for some examples of how it could be achieved e.g using combination of awk_sed if more trivial way is not exist. Thanks for help!! James -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Automatic detection and removing of steric problems
Dear PyMol users! I'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids so MD simulation of this system is crushed although of long minimization stage prior to it. I'll be very thankful if someone provide me with some script for PyMol or VMD for automatic detection of these problem (overlapped) locations and removing of the overlapped lipids detected within some cutoff radios of the protein. Thanks for help, James -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] ligand binding site visualisation
Dear Pymol users! Typically when I'm looking at the ligand binding sites (present-show of the receptor-ligand.pdb complexes all receptors non-canonical residues or the different titrable forms of the standard ones (e.g HIP-protonated HIS or ASH- protonated ASN) are recognized as the ligands as well and pymol try to find hydrogen bonds or vdv contacts of these residues with its surroundings. How I could prevent it to see only on the ligand surrounding within such pdbs? What another pymol options will be useful for the ligand sites visualization? Thanks for help, James -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
From the previous task it's OK now
small question about pymol :)
how to prevent removing TER record after editing of the structure using
pymol
e.g I used the following command to load protein-ligand complex (where
there is TER between protein and ligand) and remove hydrogens and than save
back it to new pdb where there were no more TER records
pymol $pdb -c -q -d remove hydrogens; save
${temp}/${filenamenoextention}_noH.pdb, ${filenamenoextention}
${temp}/xz.log
and smth about shell informatics:
how to scan specified string in pdb corresponded to the last line of the
ligand (which is the RES in pdb) and add after this line TER record. E.g
the basic idea:
grep -v ATOM.*\(RES\|MOL\) $pdb | # smth with sed pdb_with_TER.pdb
now I only would like to know proper reg expression in my case for GREP and
command for SED
James
2014-09-24 11:06 GMT+02:00 James Starlight jmsstarli...@gmail.com:
some additional question about shell scripting (copied from the amber
forum because I'd like to find as more sollutions of this problem as
possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
fashion.
In my case I use tleap as part of some big script to process many
models.pdb for further md simulation. Each of the model consist of pair of
CYX residues (assigned by pdb2pqr) in different positions of its sequence.
So in script I need firstly to know the number of position for each of CYX
residues of each model and than to fill this numbers to the tleap input
files for each model
in bash for one model it will be look like:
#some command to scan the sequence of model.pdb and define pair of its CYX
residues within it as the k ans i variables
printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
protein protein.parm7 protein.inpcrd\nquit ./tleap.in
so my task is only to find some command which will scan model and find
positions of the CYX within its sequence which could be put to the tleap as
two digits. It will be better to find those 2 digits using pdb as an input
and some unix command like sed or grep to find positions
I will be very thankful for any suggestions!
James
2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log
man csplit:
csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
0\|^MODEL\|^REMARK | sed -e 's/^ENDMDL/TER/g' firstmodel.pdb
sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
0\|MODEL\|REMARK\)/d' my_docking.pdb firstmodel.pdb
... shorter and one process running in stead of 3.
Cheers,
Tsjerk
--
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Re: [PyMOL] Molecular Visualisation in PyMol
Hi Gian, thank you very much! The idea to associate side chain dynamics with the its B-factor is very attractive for me! However I'm not sure how to make ensemble-like view of the side chains in accordance to its B-factors - in fact as the end of the day (night?!) I'd like to obtain representation of the conformational distribution of the selected side-chain based on simulation data projected on the receptors cartoon diagram - it should looks like the alignment of the whole ensemble (in transparency view) onto the averaged (solid-view) structure) not just a colour specter. If you know how to do it in PyMol based on one pdb please let me know. James 2014-09-22 10:16 GMT+02:00 Gianluca Santoni gianluca.sant...@ibs.fr: I did something similar once. For mainchains, you can at first calculate B-factors (similar as in crystallography) from md simulation, that would be added to your starting (or final, i don't remember) structure. then use the cartoon-putty representation to visualize your structure. You could try using something similar, like for exemple a color spectrum of b-factors,for the sidechains. In this case don't forget to exclude the N-ter and C-ter from your calculations, or they will completly flatten your spectrum. Cheers, Gian On 9/21/14 9:19 AM, James Starlight wrote: Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471; iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
On Sep 22, 2014, at 4:30 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
# dock each model to the ligand
for pdb in $receptors/*.pdb; do
filename=$(basename $pdb)
M=${filename/.pdb/}
echo Processing of ${M} is initiated...
#remove water and ions; change EMD to TER
grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g'
${dirr}/temp/${M}_clean.pdb
#superimsoposition using pymol against reference
pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi
2-280; save ./superimposed/${M}_aligned.pdb, $M
./superimposed/pymol_${M}.log
cp $ref ./superimposed
done
Glad it worked for you.
two additional questions:
1) will it possible to use more flexibility in case of the selection of
region for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?
Try `$R and resi 2-280 and ss h`. See
http://www.pymolwiki.org/index.php/Property_Selectors for more info.
(That page comes up as the very first result for me on Google with “pymol
select secondary structure” as the search term.)
2) what advantages could give me tmalign method for the superimposition
in comparison to super and ce programs? does the coordinates of the
reference will not changed after alignment of each mobile on it (like
fitting in case of super) ?
From the description here (http://www.pymolwiki.org/index.php/TMalign)
that TMalign, like CEalign, can be useful for structures in the “twilight
zone,” where sequence alignment by `align` or structural alignment by
`super` may not provide a good fit. For any of the programs, though, only
the mobile structures should move; the target/reference coordinates should
always remain unchanged.
Cheers,
Jared
James
2014-09-22 10:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
2014-09-19 20:19 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
I don’t have any experience with Profit. However, instead of using
something like” PyMOL’s `super` command as you asked, you could actually
use `super` in your shell session by launching PyMOL in command line
mode http://www.pymolwiki.org/index.php/Command_Line_Options. Of
course, you would need to modify it according to your file naming scheme,
but here’s a working example.
###
#!/bin/bash
REF=reference.pdb
# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
i=$((i+1))
done
mv mobile0.pdb $REF
# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')
# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
${M}_aligned.pdb
done
pymol mobile*_aligned.pdb
###
You could also use CEalign if you need something citable, just switch
the order of the arguments to it: `cealign $R and resi 1-110, $M`.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 19, 2014, at 6:03 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear all,
I still need some help regarding some algorithm for structural
superimposition of my mobile structures regarding one specified reference
using some fitting method (to avoid changing in the position of the
reference.pdb which is very important for me!)=something like super
command in pymol. Using ProFit I have faced with some errors during
superimposition regarding the chosing reference (in case where there were
some differences in the positions of ref and mob structures its alignment
was not perfect (the mob had not been fully aligned on the ref) obtaining
very big RMSD (20 A!) as the result although its actual value should be in
range of 2-5 A. I'll be thankful for possible sollutions of this problem
using Profit is there are users experienced with this software (mb it
should to define fitting zones or atom subsets more accurately but I have
no ideas here ) or any other alternatives which could be used as parts of
the shell script.
James
--
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Re: [PyMOL] Shell utilities for structural bioinformatics
some additional question about shell scripting (copied from the amber forum
because I'd like to find as more sollutions of this problem as possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
fashion.
In my case I use tleap as part of some big script to process many
models.pdb for further md simulation. Each of the model consist of pair of
CYX residues (assigned by pdb2pqr) in different positions of its sequence.
So in script I need firstly to know the number of position for each of CYX
residues of each model and than to fill this numbers to the tleap input
files for each model
in bash for one model it will be look like:
#some command to scan the sequence of model.pdb and define pair of its CYX
residues within it as the k ans i variables
printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
protein protein.parm7 protein.inpcrd\nquit ./tleap.in
so my task is only to find some command which will scan model and find
positions of the CYX within its sequence which could be put to the tleap as
two digits. It will be better to find those 2 digits using pdb as an input
and some unix command like sed or grep to find positions
I will be very thankful for any suggestions!
James
2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log
man csplit:
csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
0\|^MODEL\|^REMARK | sed -e 's/^ENDMDL/TER/g' firstmodel.pdb
sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
0\|MODEL\|REMARK\)/d' my_docking.pdb firstmodel.pdb
... shorter and one process running in stead of 3.
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] Access to pymol commands from the terminal
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
# dock each model to the ligand
for pdb in $receptors/*.pdb; do
filename=$(basename $pdb)
M=${filename/.pdb/}
echo Processing of ${M} is initiated...
#remove water and ions; change EMD to TER
grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g'
${dirr}/temp/${M}_clean.pdb
#superimsoposition using pymol against reference
pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi
2-280; save ./superimposed/${M}_aligned.pdb, $M
./superimposed/pymol_${M}.log
cp $ref ./superimposed
done
two additional questions:
1) will it possible to use more flexibility in case of the selection of
region for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?
2) what advantages could give me tmalign method for the superimposition in
comparison to super and ce programs? does the coordinates of the reference
will not changed after alignment of each mobile on it (like fitting in case
of super) ?
James
2014-09-22 10:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
2014-09-19 20:19 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
I don’t have any experience with Profit. However, instead of using
something like” PyMOL’s `super` command as you asked, you could actually
use `super` in your shell session by launching PyMOL in command line mode
http://www.pymolwiki.org/index.php/Command_Line_Options. Of course,
you would need to modify it according to your file naming scheme, but
here’s a working example.
###
#!/bin/bash
REF=reference.pdb
# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
i=$((i+1))
done
mv mobile0.pdb $REF
# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')
# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
${M}_aligned.pdb
done
pymol mobile*_aligned.pdb
###
You could also use CEalign if you need something citable, just switch
the order of the arguments to it: `cealign $R and resi 1-110, $M`.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 19, 2014, at 6:03 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear all,
I still need some help regarding some algorithm for structural
superimposition of my mobile structures regarding one specified reference
using some fitting method (to avoid changing in the position of the
reference.pdb which is very important for me!)=something like super
command in pymol. Using ProFit I have faced with some errors during
superimposition regarding the chosing reference (in case where there were
some differences in the positions of ref and mob structures its alignment
was not perfect (the mob had not been fully aligned on the ref) obtaining
very big RMSD (20 A!) as the result although its actual value should be in
range of 2-5 A. I'll be thankful for possible sollutions of this problem
using Profit is there are users experienced with this software (mb it
should to define fitting zones or atom subsets more accurately but I have
no ideas here ) or any other alternatives which could be used as parts of
the shell script.
James
--
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Re: [PyMOL] Molecular Visualisation in PyMol
Hi Jed, so this method is working of the ensemble of the pdb files taken from the MD simulation or NMR structure, isnt it? Could someone explain me step by step how to obtain such inputs for the PyMol (from the step when I've load my trajectory to the VMD). James 2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu: You could extract the flexible residues into one multistate object and use show all_states. So, you'd only be dealing with 2 objects - Ca and residues. Jed On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Molecular Visualisation in PyMol
I should to specify that I ask this because normally VMD didn't produce multi-state pdb from the md trajectory so it seems I need to use some plugin to load *.dcd or *.trr James 2014-09-22 13:53 GMT+04:00 James Starlight jmsstarli...@gmail.com: Hi Jed, so this method is working of the ensemble of the pdb files taken from the MD simulation or NMR structure, isnt it? Could someone explain me step by step how to obtain such inputs for the PyMol (from the step when I've load my trajectory to the VMD). James 2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu: You could extract the flexible residues into one multistate object and use show all_states. So, you'd only be dealing with 2 objects - Ca and residues. Jed On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Molecular Visualisation in PyMol
Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Academical position in field of macromolecular visualization
Hi Tsjerk , *Thank you very much for the information!I've already familiar with some Adam's works from the textbooks which were really impressed me! BTW do you know any advanced tutorials foruced on the visualization in PyMol?* *James* 2014-09-20 0:59 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, There are some research groups around that focus on scientific visualization. I recall there was someone talking about it at the Biophysical Society meeting this spring, but I don't immediately remember a name to go with it. I do know that some have taken up this kind of work commercially, like H. Adam Steinberg, who also frequents/frequented this list, and Chris Spronk (http://www.spronk3d.com). You could try to see what they do or have done and how they did it. Of course, they could possibly help you further too. Hope it helps, Tsjerk On Fri, Sep 19, 2014 at 10:09 PM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! It's probably that my next question will be slightly uncommon but presently strongly looking for new (post-doc level) position I'd like to obtain some advises from the expirienced persons like the auditory of this community. This time having PhD in theoretical biophysics I wounder whether its *in principle* possible to find an academic post-doc job focused mainly on molecular visualization and animation (as the trivial example of such job in my mind is to make a pictures and movies of the proteins and it's complexes using data from different resolution's experimental techniques and modelling). How do you think will it be easily to obtain such job for the person who's PhD was based on structural biology (experimentalist) or alternatively focused on molecular modeling and bioinformatics ? Could someone recommend me some workshops and on-line communities which could facilitate my seeking for the job? Many thanks for the suggestions, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Academical position in field of macromolecular visualization
Some important point: I've tried to scan web to locate some group involved in the molecular visualization (key words molecular graphics, molecular visualization ). As the result I've found alot of groups in the US but not in the Europe. Does it some common geographic pattern ? James 2014-09-20 10:48 GMT+04:00 James Starlight jmsstarli...@gmail.com: Hi Tsjerk , *Thank you very much for the information!I've already familiar with some Adam's works from the textbooks which were really impressed me! BTW do you know any advanced tutorials foruced on the visualization in PyMol?* *James* 2014-09-20 0:59 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, There are some research groups around that focus on scientific visualization. I recall there was someone talking about it at the Biophysical Society meeting this spring, but I don't immediately remember a name to go with it. I do know that some have taken up this kind of work commercially, like H. Adam Steinberg, who also frequents/frequented this list, and Chris Spronk (http://www.spronk3d.com). You could try to see what they do or have done and how they did it. Of course, they could possibly help you further too. Hope it helps, Tsjerk On Fri, Sep 19, 2014 at 10:09 PM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! It's probably that my next question will be slightly uncommon but presently strongly looking for new (post-doc level) position I'd like to obtain some advises from the expirienced persons like the auditory of this community. This time having PhD in theoretical biophysics I wounder whether its *in principle* possible to find an academic post-doc job focused mainly on molecular visualization and animation (as the trivial example of such job in my mind is to make a pictures and movies of the proteins and it's complexes using data from different resolution's experimental techniques and modelling). How do you think will it be easily to obtain such job for the person who's PhD was based on structural biology (experimentalist) or alternatively focused on molecular modeling and bioinformatics ? Could someone recommend me some workshops and on-line communities which could facilitate my seeking for the job? Many thanks for the suggestions, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Dear all, I still need some help regarding some algorithm for structural superimposition of my mobile structures regarding one specified reference using some fitting method (to avoid changing in the position of the reference.pdb which is very important for me!)=something like super command in pymol. Using ProFit I have faced with some errors during superimposition regarding the chosing reference (in case where there were some differences in the positions of ref and mob structures its alignment was not perfect (the mob had not been fully aligned on the ref) obtaining very big RMSD (20 A!) as the result although its actual value should be in range of 2-5 A. I'll be thankful for possible sollutions of this problem using Profit is there are users experienced with this software (mb it should to define fitting zones or atom subsets more accurately but I have no ideas here ) or any other alternatives which could be used as parts of the shell script. James 2014-09-15 18:52 GMT+04:00 James Starlight jmsstarli...@gmail.com: Hey, I've occasionally deleted my profit script which do superimposition automatically so I'll be very thankful if someone remind me profit input script syntax for my case profit -h -f script.txt ref.pdb tar.pdb should do actual superimposition where in script.txt; ATOMS CA ZONE 2-290:2-290 FIT WRITE fitted.pdb unfortunately this end with the error Starting script: 'new.profit' Unrecognised keyword: FIT Error== Fitting has not yet been performed. Finished script: 'new.profit' althought those commands made from the profit command line works perfect ProFitFIT Fitting structures... RMS: 7.134 Where I made error? James 2014-09-12 9:13 GMT+02:00 James Starlight jmsstarli...@gmail.com: Hi Jared, yes from pymol it's OK, here I've mentioned about ProFit :) but this also have been solved. ;) James 2014-09-11 19:43 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org: Hi James - What version of PyMOL are you using? For me, using Open Source PyMOL 1.7.2.0, a typical PDB file I tested ends up with more information in that column, not less, after saving from PyMOL: Before: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N After: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N1+ Are you sure the column is there in your input file, and hasn’t been removed before loading into PyMOL? Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Sep 11, 2014, at 5:36 AM, James Starlight jmsstarli...@gmail.com wrote: I guess I've passed superimpoition- it works great - with the one exception- after fitting to ref.pdb the last colum (consisted of the atom names like C, N, O etc) from the each fitted mobile.pdb has been removed. I need to keep this column on the resulted pdb because I'll use this pdb as the initial structure for the autodock docking (actually I do superimposition because I have had all input docking parameters including XYZ of the cavity for the ref structure). If the last column is missed I have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using babel. I'll thankful to everyone who have faced with the same problem and could provide me with some suggestions. Thank for help, James 2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com: Thanks Markus, I'll try to examine it! Jed, the main problem with the profit is that I need to superimpose structures in loop which are not always has the same sequence length. Is it possible to superimpose each structure based on some common criterium found for each mobile and reference automatically? Kind regards, James 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca: Shot in the dark, based on reading “ensemble of the structures” and “ProFit”: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/ CARON – Average RMSD of NMR structure ensemble Hope that helps! Markus *From:* James Starlight [mailto:jmsstarli...@gmail.com] *Sent:* Monday, September 08, 2014 6:52 AM *To:* pymol-users *Subject:* Re: [PyMOL] Access to pymol commands from the terminal Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)= because looping using ProFit might be not good for me because each time I need to provide new atom selection for the superimposition for each model in the ProFit's script file. James 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com: Boo 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly
[PyMOL] preparation of protein ligand complexes for the MD simulation
Dear Pymol users, I've decide to make a copy of this topic from the amber mail list because this problem could be solves by ones of the methods implemented in Pymol. Here I'm facing with the problem of the preparation of protein-ligand complexes for amber md simulation: Following amber's tutorial I've made parametrization of the ligand using antechamber obtaining ligand.frcmod and ligand.lib files consisted of the parameters for my ligand and its coordinates in mol2 associated with those topologies. Now I'd like to dock this ligand to the active site of the receptor using autodock vina and make further tleap processing of complex.pdb produced by autodock to obtain all input data for simulation. Here some problems: because (superimposed to the receptor cavity) ligand.pdb produced by autodock have been stripped from all hydrogen’s so its coordinates not equal to initial ligand.mol2 . How do you think will it possible to use some method of the ligand superimposition to superimpose initial ligand.mol2 (with correct corrdinates) agains docking pose produced by vina and use superimposed ligand.mol2 for the preparation of my complex? Thanks for help, James -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] preparation of protein ligand complexes for the MD simulation
Hi Fotis, thank you very much for the suggestion! Indeed I have not had such problem with the preparation structure for NAMD but in case of amber its really exist (the structure of the ligand provided in the complex with the receptor.pdb must be EXACTLY the same as it was previously parametrized using some amber program called antechamber). So I will be interesting in two options 1) to find some shell utility for superimposition of the 2 ligands in one-style command (because here I'm dealing with some script and I need to do it in loop many times) or (which is better!) 2) use pdb2pqr software (because I'm using it in the part of this script to process complex and to add hydrogens to ligand as well)- here I noticed that ligand should be provided as the separate .mol2 file (not pdb)- which is a bit not comfortable for me (because I obained all docking poses from VINA as the pdb). I guess I should here to put ligand from complex, to convert it to mol2 and proceed 2 files (receptor and ligand) to the pdb2pqr. But may be the better solution is exist? James 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas fotis.baltou...@gmail.com: Hello James, You can use the Pair Fitting wizard (Menu: Wizards=Pair Fitting) or the pair_fit command to superimpose small molecules. It's not as straightforward as protein super/align, since you have to define the atom pairs that will be superimposed, but it's fairly easy. After that, just make a selection of your receptor and your new ligand and save it as a molecule. However, I don't think you really have a problem here. Since the only issue you mention is the lack of hydrogen atoms, couldn't you just reintroduce them through some function in the AmberTools? I have no experience with Amber parameterization tools but, if they're even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they can add hydrogen atoms for you easily. Another option would be to create a PQR file, either through PDB2PQR ( http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools GUI in PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can use AMBER parameters both for proteins and for ligands (mol2 format). Your result would be the structure of your complex, with hydrogens, in the AMBER format. Hope I helped, Fotis Baltoumas 2014-09-17 13:01 GMT+03:00 James Starlight jmsstarli...@gmail.com: Dear Pymol users, I've decide to make a copy of this topic from the amber mail list because this problem could be solves by ones of the methods implemented in Pymol. Here I'm facing with the problem of the preparation of protein-ligand complexes for amber md simulation: Following amber's tutorial I've made parametrization of the ligand using antechamber obtaining ligand.frcmod and ligand.lib files consisted of the parameters for my ligand and its coordinates in mol2 associated with those topologies. Now I'd like to dock this ligand to the active site of the receptor using autodock vina and make further tleap processing of complex.pdb produced by autodock to obtain all input data for simulation. Here some problems: because (superimposed to the receptor cavity) ligand.pdb produced by autodock have been stripped from all hydrogen’s so its coordinates not equal to initial ligand.mol2 . How do you think will it possible to use some method of the ligand superimposition to superimpose initial ligand.mol2 (with correct corrdinates) agains docking pose produced by vina and use superimposed ligand.mol2 for the preparation of my complex? Thanks for help, James -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] preparation of protein ligand complexes for the MD simulation
all manual and GUI operations are not accepted here! I'm dealing with the a huge number of protein-ligand complexes (many many different proteins but only 1 ligand- so the situation is not very bad !). But what is bad that I need to dock each complex using vina and make its parametrization by amber :) James 2014-09-17 15:32 GMT+02:00 Gianluca Santoni gianluca.sant...@ibs.fr: Hi James, what usually worked for me was simply to do it manually, in editing mode with pymol. Consider that you will perform an energy minimization after, so a few 1/10 of angstroms of difference in your initial model are not a big deal, in my opinion. Cheers, Gian On 9/17/14 3:17 PM, James Starlight wrote: Hi Fotis, thank you very much for the suggestion! Indeed I have not had such problem with the preparation structure for NAMD but in case of amber its really exist (the structure of the ligand provided in the complex with the receptor.pdb must be EXACTLY the same as it was previously parametrized using some amber program called antechamber). So I will be interesting in two options 1) to find some shell utility for superimposition of the 2 ligands in one-style command (because here I'm dealing with some script and I need to do it in loop many times) or (which is better!) 2) use pdb2pqr software (because I'm using it in the part of this script to process complex and to add hydrogens to ligand as well)- here I noticed that ligand should be provided as the separate .mol2 file (not pdb)- which is a bit not comfortable for me (because I obained all docking poses from VINA as the pdb). I guess I should here to put ligand from complex, to convert it to mol2 and proceed 2 files (receptor and ligand) to the pdb2pqr. But may be the better solution is exist? James 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas fotis.baltou...@gmail.com mailto:fotis.baltou...@gmail.com: Hello James, You can use the Pair Fitting wizard (Menu: Wizards=Pair Fitting) or the pair_fit command to superimpose small molecules. It's not as straightforward as protein super/align, since you have to define the atom pairs that will be superimposed, but it's fairly easy. After that, just make a selection of your receptor and your new ligand and save it as a molecule. However, I don't think you really have a problem here. Since the only issue you mention is the lack of hydrogen atoms, couldn't you just reintroduce them through some function in the AmberTools? I have no experience with Amber parameterization tools but, if they're even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they can add hydrogen atoms for you easily. Another option would be to create a PQR file, either through PDB2PQR (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools GUI in PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can use AMBER parameters both for proteins and for ligands (mol2 format). Your result would be the structure of your complex, with hydrogens, in the AMBER format. Hope I helped, Fotis Baltoumas 2014-09-17 13:01 GMT+03:00 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com: Dear Pymol users, I've decide to make a copy of this topic from the amber mail list because this problem could be solves by ones of the methods implemented in Pymol. Here I'm facing with the problem of the preparation of protein-ligand complexes for amber md simulation: Following amber's tutorial I've made parametrization of the ligand using antechamber obtaining ligand.frcmod and ligand.lib files consisted of the parameters for my ligand and its coordinates in mol2 associated with those topologies. Now I'd like to dock this ligand to the active site of the receptor using autodock vina and make further tleap processing of complex.pdb produced by autodock to obtain all input data for simulation. Here some problems: because (superimposed to the receptor cavity) ligand.pdb produced by autodock have been stripped from all hydrogen’s so its coordinates not equal to initial ligand.mol2 . How do you think will it possible to use some method of the ligand superimposition to superimpose initial ligand.mol2 (with correct corrdinates) agains docking pose produced by vina and use superimposed ligand.mol2 for the preparation of my complex? Thanks for help, James -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control
Re: [PyMOL] Access to pymol commands from the terminal
Hey, I've occasionally deleted my profit script which do superimposition automatically so I'll be very thankful if someone remind me profit input script syntax for my case profit -h -f script.txt ref.pdb tar.pdb should do actual superimposition where in script.txt; ATOMS CA ZONE 2-290:2-290 FIT WRITE fitted.pdb unfortunately this end with the error Starting script: 'new.profit' Unrecognised keyword: FIT Error== Fitting has not yet been performed. Finished script: 'new.profit' althought those commands made from the profit command line works perfect ProFitFIT Fitting structures... RMS: 7.134 Where I made error? James 2014-09-12 9:13 GMT+02:00 James Starlight jmsstarli...@gmail.com: Hi Jared, yes from pymol it's OK, here I've mentioned about ProFit :) but this also have been solved. ;) James 2014-09-11 19:43 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org: Hi James - What version of PyMOL are you using? For me, using Open Source PyMOL 1.7.2.0, a typical PDB file I tested ends up with more information in that column, not less, after saving from PyMOL: Before: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N After: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N1+ Are you sure the column is there in your input file, and hasn’t been removed before loading into PyMOL? Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Sep 11, 2014, at 5:36 AM, James Starlight jmsstarli...@gmail.com wrote: I guess I've passed superimpoition- it works great - with the one exception- after fitting to ref.pdb the last colum (consisted of the atom names like C, N, O etc) from the each fitted mobile.pdb has been removed. I need to keep this column on the resulted pdb because I'll use this pdb as the initial structure for the autodock docking (actually I do superimposition because I have had all input docking parameters including XYZ of the cavity for the ref structure). If the last column is missed I have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using babel. I'll thankful to everyone who have faced with the same problem and could provide me with some suggestions. Thank for help, James 2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com: Thanks Markus, I'll try to examine it! Jed, the main problem with the profit is that I need to superimpose structures in loop which are not always has the same sequence length. Is it possible to superimpose each structure based on some common criterium found for each mobile and reference automatically? Kind regards, James 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca: Shot in the dark, based on reading “ensemble of the structures” and “ProFit”: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/ CARON – Average RMSD of NMR structure ensemble Hope that helps! Markus *From:* James Starlight [mailto:jmsstarli...@gmail.com] *Sent:* Monday, September 08, 2014 6:52 AM *To:* pymol-users *Subject:* Re: [PyMOL] Access to pymol commands from the terminal Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)= because looping using ProFit might be not good for me because each time I need to provide new atom selection for the superimposition for each model in the ProFit's script file. James 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com: Boo 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info
Re: [PyMOL] Shell utilities for structural bioinformatics
Hi, some new question. I need to some combination of shell utilities to split multi_model.pdb on several pdbs as well as separate command to seek multi_model.pdb and to save only this model as the separare model1.pdb. I've tried to do it using grep grep '^MODEL 1' my_docking.pdb model1.pdb but results were empty. James 2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com: Thanks you very much! James 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com: Hi Small correction to Gianlucas suggestion will direct the output to a file, overwriting the contents will direct the output to a file, appending the contents Venlig hilsen Folmer Fredslund Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr: Don't even need cat simply do grep PPC ref.pdb tar_i.pdb redirecting std out with appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e,g in my case each model after spliting consist of
MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL
i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and change
ENDMDL to TER
i've tried to do it
csplit -b %04d.pdb my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' |
grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g'
but the resulted files still consist of unused lines
BTW might the csplit be used to extract only ONE (e,g first) model from the
multi-pdb file?
James
2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi James,
These are the sort of questions that'll be answered elsewhere. Most
notably on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b %04d.pdb file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb on
several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting the contents
will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr
:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've decided to open new topic focused on the implementation of the
common shell utilities like grep awk and sed for the structural
bioinformatics tasks like processing and editing of the large sets
of pdbs.
In my current task I need to copy all lipids from one pdb (called it
ref) to another call it tar_i.pdb (both files have the same 3D shape
and
have been superimposed before that): so in that case I guess lipids
could be recognized by residue name in pdb file (PPC) as well as by
its
#4 column number (what is actually do grep). So the algorithm might
be:
select from the ref.pdb all strings where #4 column is PPC and merge
it
(by means of CAT I guess) with the tar_i.pdb. Please show me some
example of the one-line method of this realization.
Thanks,
James
--
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--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
--
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--
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Re: [PyMOL] Shell utilities for structural bioinformatics
Thank you very much! James 2014-09-12 12:36 GMT+02:00 Marko Hyvonen mh...@cam.ac.uk: On 12/09/2014 11:26, James Starlight wrote: grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK| I think you are missing few | in there: grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK and depending on the shell, you might be able get away with \ by using single quotation marks grep -v '^ROOT|^ENDROOT|^TORSDOF 0|^MODEL|^REMARK' Marko -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel:+44-(0)1223-766 044 -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
I guess I've passed superimpoition- it works great - with the one exception- after fitting to ref.pdb the last colum (consisted of the atom names like C, N, O etc) from the each fitted mobile.pdb has been removed. I need to keep this column on the resulted pdb because I'll use this pdb as the initial structure for the autodock docking (actually I do superimposition because I have had all input docking parameters including XYZ of the cavity for the ref structure). If the last column is missed I have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using babel. I'll thankful to everyone who have faced with the same problem and could provide me with some suggestions. Thank for help, James 2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com: Thanks Markus, I'll try to examine it! Jed, the main problem with the profit is that I need to superimpose structures in loop which are not always has the same sequence length. Is it possible to superimpose each structure based on some common criterium found for each mobile and reference automatically? Kind regards, James 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca: Shot in the dark, based on reading “ensemble of the structures” and “ProFit”: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/ CARON – Average RMSD of NMR structure ensemble Hope that helps! Markus *From:* James Starlight [mailto:jmsstarli...@gmail.com] *Sent:* Monday, September 08, 2014 6:52 AM *To:* pymol-users *Subject:* Re: [PyMOL] Access to pymol commands from the terminal Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)= because looping using ProFit might be not good for me because each time I need to provide new atom selection for the superimposition for each model in the ProFit's script file. James 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com: Boo 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement
Re: [PyMOL] Access to pymol commands from the terminal
Thanks Markus, I'll try to examine it! Jed, the main problem with the profit is that I need to superimpose structures in loop which are not always has the same sequence length. Is it possible to superimpose each structure based on some common criterium found for each mobile and reference automatically? Kind regards, James 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca: Shot in the dark, based on reading “ensemble of the structures” and “ProFit”: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/ CARON – Average RMSD of NMR structure ensemble Hope that helps! Markus *From:* James Starlight [mailto:jmsstarli...@gmail.com] *Sent:* Monday, September 08, 2014 6:52 AM *To:* pymol-users *Subject:* Re: [PyMOL] Access to pymol commands from the terminal Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)= because looping using ProFit might be not good for me because each time I need to provide new atom selection for the superimposition for each model in the ProFit's script file. James 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com: Boo 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
Thanks you very much! James 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com: Hi Small correction to Gianlucas suggestion will direct the output to a file, overwriting the contents will direct the output to a file, appending the contents Venlig hilsen Folmer Fredslund Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr: Don't even need cat simply do grep PPC ref.pdb tar_i.pdb redirecting std out with appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)= because looping using ProFit might be not good for me because each time I need to provide new atom selection for the superimposition for each model in the ProFit's script file. James 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com: Boo 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a): Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, align.profit or die Cannot open file align.profit\n; print $PROFIT ATOMS CA\n; print $PROFIT ZONE 34-513:1-480\n; print $PROFIT FIT\n; print $PROFIT WRITE $folder/$dir/$pdbnew\n; close $PROFIT; shouldn't it? that that file is provided to 1 command line `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb $folder/$dir/$pdbnew`; where 2hi4.pdb is my ref $pdbnew variable assosiated with the target pdb one question about align.profit: will the output aligned mobile.pdb consist of all atoms? I've found that only CA atoms are used for the superimposition print $PROFIT ATOMS CA\n; James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Thanks Matthew,
I'll try to use this opportunity! BTW does anybody knows some simple Linux
utility to perform structural superimposition of 2 pdbs and obtain the
superimposed (target.pdb) in separate pdb file? This time I'm writing big
docking script where I need to superimpose each receptor against some
reference.pdb and use superimposed pdb for docking. Because I'll work with
huge pdb datasets I relly don’t want to call python each time.
James
2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You could make a python script that import pymol and does what you want
from there.
Some thing like this (untested);
import __main__
__main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
import pymol
pymol.finish_launching()
from pymol import cmd
reffile = sys.argv[1]
tarfile = sys.argv[2]
outfile = sys.argv[3]
cmd.load(reffile, 'ref')
cmd.load(tarfile, 'tar')
cmd.align('ref', 'tar')
cmd.save(outfile, 'ref')
Then on the command line call it like: python my_align.py reffile.pdb
target.pdb output.pdb
On 09/04/2014 11:06 AM, James Starlight wrote:
thank you very much!
so now only my question regarding the usage of the pymol commands in
command line is still open
BTW could someone suggest me the shell utility to make quick
superimposition of the tar.pdb to ref.pdb and save superimposed tar.pdb as
the separate pdb (the TMalign is not good because it produce pdb with both
merged layers (and its backbone trace only) as the result if -o flagg is
provided)
Kind regards,
Gleb
2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You can use sed
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
's/^END/TER/g' merged.pdb
On 09/04/2014 10:54 AM, James Starlight wrote:
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
Use the -h flag with grep to suppress the filename.
Also, you don't need to pipe to cat, you can write directly to the file.
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
On 09/04/2014 10:38 AM, James Starlight wrote:
..and one question about grep (really didn't find it in the tutorial)
using
grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb
I've obtained good pdb BUT each line prior to the ATOM the name of the
pdb of the previous files have been added eg:
tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306 92.256
0.00 0.00 N
tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836 93.529
0.00 0.00 C
tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339 93.708
0.00 0.00 C
tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297 93.674
0.00 0.00 O
tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984 94.698
0.00 0.00 C
tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171 95.960
0.00 0.00 C
tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481 8.453 95.823
0.00 0.00 O
tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257 8.362 97.046
0.00 0.00 O1-
tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033 93.580
0.00 0.00 H
tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496 6.916 94.504
0.00 0.00 H
tarr_se.pdb:ATOM 11 HB3 ASP X 1 36.648 7.969 94.970
0.00 0.00 H
such pattern are always produced by grep
so I'd like that tarr_se.pdb: have not been included (of course I can
it remove easily after merging but this step is not good for me :) )
Also i'll be very thankful for any useful grep awk sed tutorial in case
of the bioinformatics application
James
2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com:
one question :)
could someone explain me the ussage the pymol commands from the shell
on the example
e.g i need to load 2 pdbs in pymol make its superimposition and than
save one of the superimposed pdb
like
load ref.pdb tar.pdb
super tar, ref
save tar tar_superimposed.pdb
I've tried to do part of this using
pymol ref.pdb tarr.pdb -cd super tarr ref
but eventually obtained error
James
2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks Guys!
I'll check the tutorials.
All the best,
James
2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:
(sed '1d' protein.pdb; sed '1d' lipid.pdb) merged.pdb
--or--
tail -q -n '+2' protein.pdb lipid.pdb merged.pdb
-David
--
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Re: [PyMOL] Access to pymol commands from the terminal
should to add
than I've used both TMalign and mammoth utilities but didn't understand how
to obtain superimposed output as the full-atomic pdb's. I will be thankful
if someone could share with me its experience :)
James
2014-09-05 12:00 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks Matthew,
I'll try to use this opportunity! BTW does anybody knows some simple Linux
utility to perform structural superimposition of 2 pdbs and obtain the
superimposed (target.pdb) in separate pdb file? This time I'm writing big
docking script where I need to superimpose each receptor against some
reference.pdb and use superimposed pdb for docking. Because I'll work with
huge pdb datasets I relly don’t want to call python each time.
James
2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You could make a python script that import pymol and does what you want
from there.
Some thing like this (untested);
import __main__
__main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
import pymol
pymol.finish_launching()
from pymol import cmd
reffile = sys.argv[1]
tarfile = sys.argv[2]
outfile = sys.argv[3]
cmd.load(reffile, 'ref')
cmd.load(tarfile, 'tar')
cmd.align('ref', 'tar')
cmd.save(outfile, 'ref')
Then on the command line call it like: python my_align.py reffile.pdb
target.pdb output.pdb
On 09/04/2014 11:06 AM, James Starlight wrote:
thank you very much!
so now only my question regarding the usage of the pymol commands in
command line is still open
BTW could someone suggest me the shell utility to make quick
superimposition of the tar.pdb to ref.pdb and save superimposed tar.pdb as
the separate pdb (the TMalign is not good because it produce pdb with both
merged layers (and its backbone trace only) as the result if -o flagg is
provided)
Kind regards,
Gleb
2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You can use sed
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
's/^END/TER/g' merged.pdb
On 09/04/2014 10:54 AM, James Starlight wrote:
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
Use the -h flag with grep to suppress the filename.
Also, you don't need to pipe to cat, you can write directly to the file.
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
On 09/04/2014 10:38 AM, James Starlight wrote:
..and one question about grep (really didn't find it in the
tutorial)
using
grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb
I've obtained good pdb BUT each line prior to the ATOM the name of the
pdb of the previous files have been added eg:
tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306 92.256
0.00 0.00 N
tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836 93.529
0.00 0.00 C
tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339 93.708
0.00 0.00 C
tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297 93.674
0.00 0.00 O
tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984 94.698
0.00 0.00 C
tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171 95.960
0.00 0.00 C
tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481 8.453 95.823
0.00 0.00 O
tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257 8.362 97.046
0.00 0.00 O1-
tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033 93.580
0.00 0.00 H
tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496 6.916 94.504
0.00 0.00 H
tarr_se.pdb:ATOM 11 HB3 ASP X 1 36.648 7.969 94.970
0.00 0.00 H
such pattern are always produced by grep
so I'd like that tarr_se.pdb: have not been included (of course I can
it remove easily after merging but this step is not good for me :) )
Also i'll be very thankful for any useful grep awk sed tutorial in
case of the bioinformatics application
James
2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com:
one question :)
could someone explain me the ussage the pymol commands from the shell
on the example
e.g i need to load 2 pdbs in pymol make its superimposition and than
save one of the superimposed pdb
like
load ref.pdb tar.pdb
super tar, ref
save tar tar_superimposed.pdb
I've tried to do part of this using
pymol ref.pdb tarr.pdb -cd super tarr ref
but eventually obtained error
James
2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks Guys!
I'll check the tutorials.
All the best,
James
2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:
(sed '1d' protein.pdb; sed '1d' lipid.pdb) merged.pdb
--or--
tail -q -n '+2' protein.pdb lipid.pdb
Re: [PyMOL] Access to pymol commands from the terminal
Thanks Tsjerk!
Today I've tried some software of pairs alignment (like ce, tmalign and
mammoth) and found that it's not good for me because the positions of
reference and target are both altered as the result of the alignment by
means of the rotational matrix superimposition method. In my case I need to
move completely atoms of ref.pdb to the tar.pdb positions (whats pymol's
super command is actual do!) because I need to copy some docking
parameters (like docking box xyz vectors) from ref to each of the target.
So I'd be very thankful if someone shown me most trivial case to use super
command from the Pymol from the terminal in a few-line method (I really
wiuld like to avoid some python scripts from my bash) like:
load ref.pdb tar.pdb
super tar.pdb ref.pdb
save tar.pdb
Thanks for help,
James
2014-09-05 13:36 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi James,
I have a light version for fitting gromacs' gro files. No time to adapt
that now for PDB, but it's not too hard.
./qfit.py source.gro target.gro output.gro
Hope it helps,
Tsjerk
On Fri, Sep 5, 2014 at 12:31 PM, James Starlight jmsstarli...@gmail.com
wrote:
should to add
than I've used both TMalign and mammoth utilities but didn't understand
how to obtain superimposed output as the full-atomic pdb's. I will be
thankful if someone could share with me its experience :)
James
2014-09-05 12:00 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks Matthew,
I'll try to use this opportunity! BTW does anybody knows some simple
Linux utility to perform structural superimposition of 2 pdbs and obtain
the superimposed (target.pdb) in separate pdb file? This time I'm writing
big docking script where I need to superimpose each receptor against some
reference.pdb and use superimposed pdb for docking. Because I'll work with
huge pdb datasets I relly don’t want to call python each time.
James
2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You could make a python script that import pymol and does what you want
from there.
Some thing like this (untested);
import __main__
__main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
import pymol
pymol.finish_launching()
from pymol import cmd
reffile = sys.argv[1]
tarfile = sys.argv[2]
outfile = sys.argv[3]
cmd.load(reffile, 'ref')
cmd.load(tarfile, 'tar')
cmd.align('ref', 'tar')
cmd.save(outfile, 'ref')
Then on the command line call it like: python my_align.py reffile.pdb
target.pdb output.pdb
On 09/04/2014 11:06 AM, James Starlight wrote:
thank you very much!
so now only my question regarding the usage of the pymol commands in
command line is still open
BTW could someone suggest me the shell utility to make quick
superimposition of the tar.pdb to ref.pdb and save superimposed tar.pdb as
the separate pdb (the TMalign is not good because it produce pdb with both
merged layers (and its backbone trace only) as the result if -o flagg is
provided)
Kind regards,
Gleb
2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
You can use sed
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
's/^END/TER/g' merged.pdb
On 09/04/2014 10:54 AM, James Starlight wrote:
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:
Use the -h flag with grep to suppress the filename.
Also, you don't need to pipe to cat, you can write directly to the
file.
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb
merged.pdb
On 09/04/2014 10:38 AM, James Starlight wrote:
..and one question about grep (really didn't find it in the
tutorial)
using
grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |cat
merged.pdb
I've obtained good pdb BUT each line prior to the ATOM the name of
the pdb of the previous files have been added eg:
tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306 92.256
0.00 0.00 N
tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836 93.529
0.00 0.00 C
tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339 93.708
0.00 0.00 C
tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297 93.674
0.00 0.00 O
tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984 94.698
0.00 0.00 C
tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171 95.960
0.00 0.00 C
tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481 8.453 95.823
0.00 0.00 O
tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257 8.362 97.046
0.00 0.00 O1-
tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033 93.580
0.00 0.00 H
tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496 6.916 94.504
0.00 0.00 H
tarr_se.pdb:ATOM 11 HB3
[PyMOL] Shell utilities for structural bioinformatics
Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
Hi Jed!
thanks for the advise!
As I understood some commands like FIT and WRITE should be provided being
INSIDE of the profit to obtain pdb output. Does it possible to do it in one
line style from bash like profit ref tar output etc ? BTW profit send
errors when I try to fit mob to ref and when residue number is mismatched.
Is it possible to ignore all atoms but not amino-acids from the both pdbs
(e,g in my case ref consist of the lipids as well which I need to use on
further step to copy from ref to superimposed tar) ?
THF,
James
2014-09-05 18:41 GMT+02:00 Jed Goldstone jedg...@gmail.com:
I have used ProFit for that task, from Andrew Martin's group at UCL. It
does least-squares fitting, so it's reasonably quick.
http://www.bioinf.org.uk/software/profit/index.html
Jed
On 9/5/2014 6:00 AM, James Starlight wrote:
Thanks Matthew,
I'll try to use this opportunity! BTW does anybody knows some simple
Linux utility to perform structural superimposition of 2 pdbs and obtain
the superimposed (target.pdb) in separate pdb file? This time I'm
writing big docking script where I need to superimpose each receptor
against some reference.pdb and use superimposed pdb for docking. Because
I'll work with huge pdb datasets I relly don’t want to call python each
time.
James
2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu
mailto:mp...@pitt.edu:
You could make a python script that import pymol and does what you
want from there.
Some thing like this (untested);
import __main__
__main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
import pymol
pymol.finish_launching()
from pymol import cmd
reffile = sys.argv[1]
tarfile = sys.argv[2]
outfile = sys.argv[3]
cmd.load(reffile, 'ref')
cmd.load(tarfile, 'tar')
cmd.align('ref', 'tar')
cmd.save(outfile, 'ref')
Then on the command line call it like: python my_align.py
reffile.pdb target.pdb output.pdb
On 09/04/2014 11:06 AM, James Starlight wrote:
thank you very much!
so now only my question regarding the usage of the pymol commands
in command line is still open
BTW could someone suggest me the shell utility to make quick
superimposition of the tar.pdb to ref.pdb and save superimposed
tar.pdb as the separate pdb (the TMalign is not good because it
produce pdb with both merged layers (and its backbone trace only)
as the result if -o flagg is provided)
Kind regards,
Gleb
2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu
mailto:mp...@pitt.edu:
You can use sed
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed
-e 's/^END/TER/g' merged.pdb
On 09/04/2014 10:54 AM, James Starlight wrote:
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb
merged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:41 GMT+02:00 Matthew Baumgartner
mp...@pitt.edu mailto:mp...@pitt.edu:
Use the -h flag with grep to suppress the filename.
Also, you don't need to pipe to cat, you can write
directly to the file.
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb
lipids.pdbmerged.pdb
On 09/04/2014 10:38 AM, James Starlight wrote:
..and one question about grep (really didn't find it in
the tutorial)
using
grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb
|catmerged.pdb
I've obtained good pdb BUT each line prior to the ATOM
the name of the pdb of the previous files have been
added eg:
tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306
92.256 0.00 0.00 N
tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836
93.529 0.00 0.00 C
tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339
93.708 0.00 0.00 C
tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297
93.674 0.00 0.00 O
tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984
94.698 0.00 0.00 C
tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171
95.960 0.00 0.00 C
tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481
8.453 95.823 0.00 0.00 O
tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257
8.362 97.046 0.00 0.00 O1-
tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033
93.580 0.00 0.00 H
tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496
6.916 94.504 0.00 0.00 H
Re: [PyMOL] Access to pymol commands from the terminal
Hi Tsjerk, Thanks alot! Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted of the unusuall first line which should be deleated before it merging (in my case it's the HEADER lala.pdb). could you suggest me the combination of grep sed command which should be used to deleate the first line from both pdbs and than merge it in one-command method? Many thanks, James 2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You can use pymol -cd pymolcommands. See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v ^ATOM.*SOL in.pdb out.pdb To remove NA+/CL- too grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb out.pdb The fitting is a bit more cumbersome :) Hope it helps, Tsjerk On Thu, Sep 4, 2014 at 10:19 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd like to find possibilities for running of some pymol commands from the terminal. For instance in my case I' d like perform 2 simple steps (both in terminal not in the pymol GUI) to remove water and ions from my target input pdb (typical I do it via gromacs editconf) superimpose target.pdb against reference.pdb ( i do it by means of tmalign utility) Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
one question :) could someone explain me the ussage the pymol commands from the shell on the example e.g i need to load 2 pdbs in pymol make its superimposition and than save one of the superimposed pdb like load ref.pdb tar.pdb super tar, ref save tar tar_superimposed.pdb I've tried to do part of this using pymol ref.pdb tarr.pdb -cd super tarr ref but eventually obtained error James 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com: Thanks Guys! I'll check the tutorials. All the best, James 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net: (sed '1d' protein.pdb; sed '1d' lipid.pdb) merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight jmsstarli...@gmail.com wrote: Hi Tsjerk, Thanks alot! Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted of the unusuall first line which should be deleated before it merging (in my case it's the HEADER lala.pdb). could you suggest me the combination of grep sed command which should be used to deleate the first line from both pdbs and than merge it in one-command method? Many thanks, James 2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You can use pymol -cd pymolcommands. See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v ^ATOM.*SOL in.pdb out.pdb To remove NA+/CL- too grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb out.pdb The fitting is a bit more cumbersome :) Hope it helps, Tsjerk On Thu, Sep 4, 2014 at 10:19 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd like to find possibilities for running of some pymol commands from the terminal. For instance in my case I' d like perform 2 simple steps (both in terminal not in the pymol GUI) to remove water and ions from my target input pdb (typical I do it via gromacs editconf) superimpose target.pdb against reference.pdb ( i do it by means of tmalign utility) Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymol commands from the terminal
thanks! and do I need to pipe the below command to smth grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb if I need to change 'END' to 'TER' in the merged.pdb ? 2014-09-04 16:54 GMT+02:00 James Starlight jmsstarli...@gmail.com: thanks! and do I need to pipe the below command to smth grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb if I need to change 'END' to 'TER' in the merged.pdb ? 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu: Use the -h flag with grep to suppress the filename. Also, you don't need to pipe to cat, you can write directly to the file. grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb On 09/04/2014 10:38 AM, James Starlight wrote: ..and one question about grep (really didn't find it in the tutorial) using grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb I've obtained good pdb BUT each line prior to the ATOM the name of the pdb of the previous files have been added eg: tarr_se.pdb:ATOM 1 N ASP X 1 35.722 8.306 92.256 0.00 0.00 N tarr_se.pdb:ATOM 2 CA ASP X 1 35.252 8.836 93.529 0.00 0.00 C tarr_se.pdb:ATOM 3 C ASP X 1 35.797 10.339 93.708 0.00 0.00 C tarr_se.pdb:ATOM 4 O ASP X 1 34.979 11.297 93.674 0.00 0.00 O tarr_se.pdb:ATOM 5 CB ASP X 1 35.593 7.984 94.698 0.00 0.00 C tarr_se.pdb:ATOM 6 CG ASP X 1 34.692 8.171 95.960 0.00 0.00 C tarr_se.pdb:ATOM 7 OD1 ASP X 1 33.481 8.453 95.823 0.00 0.00 O tarr_se.pdb:ATOM 8 OD2 ASP X 1 35.257 8.362 97.046 0.00 0.00 O1- tarr_se.pdb:ATOM 9 HA ASP X 1 34.180 9.033 93.580 0.00 0.00 H tarr_se.pdb:ATOM 10 HB2 ASP X 1 35.496 6.916 94.504 0.00 0.00 H tarr_se.pdb:ATOM 11 HB3 ASP X 1 36.648 7.969 94.970 0.00 0.00 H such pattern are always produced by grep so I'd like that tarr_se.pdb: have not been included (of course I can it remove easily after merging but this step is not good for me :) ) Also i'll be very thankful for any useful grep awk sed tutorial in case of the bioinformatics application James 2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com: one question :) could someone explain me the ussage the pymol commands from the shell on the example e.g i need to load 2 pdbs in pymol make its superimposition and than save one of the superimposed pdb like load ref.pdb tar.pdb super tar, ref save tar tar_superimposed.pdb I've tried to do part of this using pymol ref.pdb tarr.pdb -cd super tarr ref but eventually obtained error James 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com: Thanks Guys! I'll check the tutorials. All the best, James 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net: (sed '1d' protein.pdb; sed '1d' lipid.pdb) merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight jmsstarli...@gmail.com wrote: Hi Tsjerk, Thanks alot! Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted of the unusuall first line which should be deleated before it merging (in my case it's the HEADER lala.pdb). could you suggest me the combination of grep sed command which should be used to deleate the first line from both pdbs and than merge it in one-command method? Many thanks, James 2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You can use pymol -cd pymolcommands. See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v ^ATOM.*SOL in.pdb out.pdb To remove NA+/CL- too grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb out.pdb The fitting is a bit more cumbersome :) Hope it helps, Tsjerk On Thu, Sep 4, 2014 at 10:19 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd like to find possibilities for running of some pymol commands from the terminal. For instance in my case I' d like perform 2 simple steps (both in terminal not in the pymol GUI) to remove water and ions from my target input pdb (typical I do it via gromacs editconf) superimpose target.pdb against reference.pdb ( i do it by means of tmalign utility) Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org
[PyMOL] Making nmr-like ensemble from several pdbs
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
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Re: [PyMOL] Making nmr-like ensemble from several pdbs
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case of each model and obtained back ensemble with
the processed conformers.
At this time using such nmr ensemble I've faced with the below error
FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
I don't why this error occurs (I have not this in case of ONE model from
the ensemble)
James
2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end
of each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
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Panepistimioupoli-Zografou
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email: tev...@pharm.uoa.gr
teva...@gmail.com
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*- Ernest Rutherford*
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Re: [PyMOL] Making nmr-like ensemble from several pdbs
is it working here? https://www.sendspace.com/file/8i0aqo James 2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de: On 27/08/14 07:56, James Starlight wrote: Hi both of them are present in my ensemble. the problem is not here- if it possible i could upload the ensemble.pdb to some server if someone could check it. James Hi, Go for some paste bins or do a gist on github. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
legitimate chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier A, B, etc. to
denote different models of the same monomer (as in e.g. 2TRX). Make sure
you supply only the one you want. For NMR structures, you get a window
where you can choose which model to use.
i guess it indicate that in principle some ensembles are possible as the
input :) Alternatively do you know any other tools (software) for the
processing of the ensembles with such options for the analysis?
James
2014-08-27 15:05 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
On 27 August 2014 15:43, James Starlight jmsstarli...@gmail.com wrote:
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
for the titrable residues in case of each model and obtained back ensemble
with the processed conformers.
I think H++ server processes one structure per job. Where did you find
that you can upload an ensemble?
At this time using such nmr ensemble I've faced with the below error
FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
I don't why this error occurs (I have not this in case of ONE model from
the ensemble)
James
2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end
of each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1
nmr-like object. Could you suggest me how this script could be modified to
make alignment (or it's better structural alignment) of all pdbs against
first loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
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==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
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[PyMOL] Saving trajectory outputs
Dear Pymol Users! I wounder whether it will be possible to save big ensemble of the loaded into pymol Pdb's files as the trajectory output (like dcd format) what are actually can be performed by vmd (e.g by means of http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/). The problem in last case is that I don't know how to perform superimposition of my conformers agains refeence frame (alternatively what is easily performed in pymol). I'll be thankful for any suggestions. Best wishes, James -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] python scripting in pymol
Dear PyMol users! I'm learning of the python scripting for the solution of typical structural bioinformatics problems. This time I'd like to integrate in pymol simple script which will search for the selected motifs (just several amino acids situated in adjacent positions along the sequence) and marked selection data assuming that I'm working with ensemble of homologue proteins having common motifs. Could someone provide me with the example of such script included pymol syntax in code? During further steps I'd like to improve such script for searching of motis situated in adjacent space position in 3D pdb structures but not in its sequences. Thanks for help, James -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] AutoDock plugin
Dear PyMol users! I've forced with the problem of the installation of AutoDock plugin pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've tried to install it manually from the downloaded py script but at the starting of pymol below error has bbeen appeared Unable to initialize plugin 'autodock' (pmg_tk.startup.autodock). Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin). Also I've tried to search for the plugin in the pymol repositories but have not found it. How it could be solved ? James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] AutoDock plugin
Thomas, Thanks for suggestions. 1)I have installed Numpy. 2) File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File /usr/share/pyshared/pmg_tk/startup/autodock_plugin.py, line 62, in module from numpy import * File /usr/share/pyshared/numpy/__init__.py, line 137, in module import add_newdocs File /usr/share/pyshared/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/share/pyshared/numpy/lib/__init__.py, line 4, in module from type_check import * File /usr/share/pyshared/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /usr/share/pyshared/numpy/core/__init__.py, line 5, in module import multiarray ImportError: No module named multiarray What package is needed which consist of multiarray module ? James 2013/12/6 Thomas Holder spel...@users.sourceforge.net Hi James, import pmg_tk.startup.autodock_plugin should tell you what's wrong. My next guess is that you don't have numpy installed. For the missing bonds in your example, PyMOL thinks those atoms are cations because of the symbol in the last column. By default, PyMOL doesn't make bonds to cations. But this will work: PyMOLunset pdb_unbond_cations, PyMOLload example.pdb Hope that helps. Cheers, Thomas On 06 Dec 2013, at 11:04, James Starlight jmsstarli...@gmail.com wrote: Thomas, I have this problem within the recent pymol 1.6.0.0 version installed on Linux Debian (all others plugins work correct. Also Autodock plugin is not seen in the repository) By the way in this Pymol version I've forced with some problems with the ligands representation. For example I've obtained typical docking output from the AutoDock consisted of 10 poses (in separate models) but some atoms of this ligands is visualized as a blank atoms. Below the atoms of the one model are provided as the example. HETATM1 CAG P0G R 1 -0.073 -2.031 12.923 1.00 0.00 .001 A HETATM2 CAH P0G R 1 -0.624 -2.630 11.797 1.00 0.00 .001 A HETATM3 CAI P0G R 1 0.713 -0.894 12.787 1.00 0.00 .007 A HETATM4 CAJ P0G R 1 -0.383 -2.091 10.540 1.00 0.00 .007 A HETATM5 CAW P0G R 1 -2.339 3.404 5.677 1.00 0.00 .008 A HETATM6 CAL P0G R 1 -1.712 3.845 4.518 1.00 0.00 .015 A HETATM7 CAK P0G R 1 -1.825 5.176 4.131 1.00 0.00 .039 A HETATM8 CAB P0G R 1 0.291 2.102 8.752 1.00 0.00 .046 C HETATM9 CAC P0G R 1 -1.618 0.656 9.433 1.00 0.00 .046 C HETATM 10 CAA P0G R 1 1.806 0.879 11.409 1.00 0.00 .049 C HETATM 11 CAV P0G R 1 0.396 -0.946 10.403 1.00 0.00 .050 A HETATM 12 CAT P0G R 1 0.950 -0.354 11.529 1.00 0.00 .056 A HETATM 13 NAP P0G R 1 -0.642 0.506 7.208 1.00 0.00 .064 N HETATM 14 CAO P0G R 1 0.652 -0.375 9.023 1.00 0.00 .077 C HETATM 15 CAU P0G R 1 -2.570 6.062 4.900 1.00 0.00 .095 A HETATM 16 CAX P0G R 1 -3.197 5.612 6.048 1.00 0.00 .102 A HETATM 17 CAY P0G R 1 -3.084 4.294 6.426 1.00 0.00 .107 A HETATM 18 CBA P0G R 1 -0.335 0.720 8.612 1.00 0.00 .122 C HETATM 19 HAQ P0G R 1 -3.677 7.418 6.890 1.00 0.00 .169 H HETATM 20 CAZ P0G R 1 -2.233 1.990 6.093 1.00 0.00 .179 C HETATM 21 HAF P0G R 1 -2.600 0.245 5.251 1.00 0.00 .210 H HETATM 22 HAE P0G R 1 -2.798 7.416 3.572 1.00 0.00 .217 H HETATM 23 CAS P0G R 1 -4.971 5.977 7.513 1.00 0.00 .246 C HETATM 24 CAN P0G R 1 -0.768 1.610 6.272 1.00 0.00 .269 C HETATM 25 OAD P0G R 1 -5.901 6.691 7.854 1.00 0.00 .271 O HETATM 26 CAM P0G R 1 -4.980 4.505 7.870 1.00 0.00 .278 C HETATM 27 2HAP P0G R 1 -1.522 0.012 7.182 1.00 0.00 .278 H HETATM 28 3HAP P0G R 1 0.062 -0.118 6.840 1.00 0.00 .278 H HETATM 29 NAQ P0G R 1 -3.925 6.442 6.827 1.00 0.00 .321 N HETATM 30 OAR P0G R 1 -3.718 3.912 7.572 1.00 0.00 .339 O HETATM 31 OAE P0G R 1 -2.682 7.366 4.523 1.00 0.00 .358 O HETATM 32 OAF P0G R 1 -2.799 1.167 5.067 1.00 0.00 .389 O 2013/12/6 Thomas Holder spel...@users.sourceforge.net Hi James, is it recent version of PyMOL, or recent version of Windows which makes trouble? On Windows, the plugin tries to write to the PyMOL installation folder, which fails if you don't have write permissions there. This needs to be fixed, the plugin should write to the users folder also on Windows. Cheers, Thomas On 06 Dec 2013, at 08:47, James Starlight jmsstarli...@gmail.com wrote: Dear
Re: [PyMOL] Working with the pdb ensemble
Hi Jared, The issue is that the all ligands are copied in one sele (and than extracted to one object). Consequently I'd like to split it to separate objects as the lig1.pdb lig2.pdb etc James 2013/12/7 Sampson, Jared jared.samp...@nyumc.org Hi James - If I understand you correctly, you just need to give a selection argument to the save command. save ligand1.pdb, sele1 save ligand2.pdb, sele2 etc... See http://pymolwiki.org/index.php/Save for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd be thankfull if you provide me with the easliest way how I could save selection to the separate pdbs. For example I've loaded 10 pdbs of the receptor and selected from in each 10 ligands. This selection is defined in one object (extracted or coppied from sele). How I could save it as 10 pdbs? Also I have a question about addtion of the hyrogens to each ligand in ensemble. How I could add hydrogens in accordance to the specified protonation states of the ligands (manually providing total charge)? Thanks for help, James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Rendering in pymol
Der Pymol users! I wounder to know if it possible to increase rendering rate mainly at the expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in the hyper-threading mode) I've spend ~ 2 hours to render image consisted of ensemble of conformations (~ 30 aligned pdbs) using only CPUs. set ray_trance mode, 1 ray 3000 png ./1.png Does it possible to add some loading to the gpu as well? James -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] RMSD calculation for the pdb ensemble
Dear PyMol users! I'm looking for python script which would perform the 1- loading ensemble of the pdbs to the pymol (assuming that it could be done by loadDir script) 2- Perform structural alighnemnt of all loaded structures against reference 0.pdb by means of buit-in TMalighn module this could be done by means of for loop I suppose 3- wtite to the ./output the pdbs which are differ agains reference (0.pdb) strongly on the selected RMSD value (e.g I have 100 structures extrracted from MD trajectory. I define in my script rmds=1.0 and I'd like that the only structures have been writed to the ./output wich have 1 A, 2 A, 3 A (value differ on the 1 A as defined in script) etc rmsd agains reference (0.pdb). As the result I'd like to select only small part of the conformers with the uniform RSMD difference Don't known how to script it :) Thanks for any usefull examples, James -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Caver 3.0 pugin
Hi Stephen, you should try lattest CAVER which could be downloaded from http://www.caver.cz before installing it via Pymol plugin menu, you should to open caver-3.0-1.py and find here CAVER3_LOCATION = directory/where/caver3/is/located and modify this on your path providing it to the jar file directly ( in this version there is no jar path in pymol plugin itself). Does anyone use it for the analysis of the ligand sites? I've test it with the GPCR and found 3 possible pathways. I'n not sure how It have been clustered but now I'n looking for the method for the steered MD along caver-predicted pathes James 2013/11/17 Stephen P. Molnar s.mol...@sbcglobal.net I would be interested in just how the problem has been solved! I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL v-1.6.0.0 compiled from the latest svn and functioning perfectly on my system. Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without any complaints. Yet when I try to use the plugin I get: ERROR: Directory incorrectly specified -plugin.jar not found, check directory/where/jar/with/plugin/is/locate/Carver2_1.jar Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory. Also other plugins are working without complaint. This is exactly the way the plug was working the last time that I attempted its installation and use. On 11/15/2013 03:14 PM, James Starlight wrote: This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight jmsstarli...@gmail.com Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariatewww.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Caver 3.0 pugin
Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Caver 3.0 pugin
This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight jmsstarli...@gmail.com Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Automatic mutation introduction
Thanks! I'll try all pf this possibilities- especially I'm interesting in Modeller because its 1) python-based and 2) produce suitable input for MD (fixing side-chains or loops missed in the X-ray input data) James 2013/11/11 Ron Jacak ron.ja...@gmail.com Hi James, SCWRL is a good suggestion. You may also want to take a look at Rosetta ( https://www.rosettacommons.org/). It uses the Dunbrack 2010 rotamer library but also includes a dozen or so other score terms to aid in repacking and minimizing mutations. There's also a server ( http://rosettadesign.med.unc.edu/), since the installation and compilation can take some time. Best, -Ron On Nov 10, 2013, at 2:27 PM, James Starlight wrote: Dear PyMol users! I'm looking for the possible python script which using the pymol source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues would be backbone dependent or taken from the existing rotamer libraries (although its not essence because I can run minimization on the mutants) Previously I've done such tasks with selectivity mutations via pymol-GUI but now I'd like to obtain big series of the mutant of studied protein for further examinations of such mutants by means of molecular dynamics simulation. Could someone provide me with such script if it could not be very complicated to make it? Thanks for help, James -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Automatic mutation introduction
Dear PyMol users! I'm looking for the possible python script which using the pymol source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues would be backbone dependent or taken from the existing rotamer libraries (although its not essence because I can run minimization on the mutants) Previously I've done such tasks with selectivity mutations via pymol-GUI but now I'd like to obtain big series of the mutant of studied protein for further examinations of such mutants by means of molecular dynamics simulation. Could someone provide me with such script if it could not be very complicated to make it? Thanks for help, James -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Cartoon transparency
Dear PyMol users! I want to set transparency on the selected carton region of my protein ( I have closed GFP barell with the chromophore inside it so I'd like set transparency of some beta-shits to make chromophore easily visible ). In PyMol I've selected region corresponded to that Beta-sheets and than used set cartoon_transparency, 0.5, sele unfortunatelly there were no any changes after this :( How I could solve it ? Thanks for help, James -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] sorting pdb ensembles based on rmsd
Dear PyMol users! I have a set of conformations extracted from the MD trajectory (on the equal time-steps). After loading of all that pdb's into pymol (each conformer= separate pdb file) I want to sort that structures based on the RMSD relative to the reference conformer (e.g step0.pdb ) in the selected range (e.g select and sort only structures with RMSD = 0.5 to the 0.pdb. So if I have 100 conformers I want that pymol select only 5 structures with rmsd (measured by TMalign plugin for instance) to reference equal to 0.5, 1, 1.5, 2.0, 2.5 and 3.0 Angstroms, respectively). Does it possible to make such sorting ? James -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Visualization of the protein-ligand interactions
Dear Pymol users! I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. Thanks for help, James -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Visualization of the protein-ligand interactions
Thomas, thanks for help! As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ? PoseView is used as the separate software or web server http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar interactions both in pymol as well as via pose view). James 2013/4/24 Thomas Evangelidis teva...@gmail.com I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Fwd: Visualization of the protein-ligand interactions
Thomas, actually I used very routine way. Firstly I've extract conformers of protein-ligand complexes from the trajectory. Than I've loaded it into pymol and visualize possible interactions. Than I've selected most representative conformers and loaded it separately into pose view to obtain 2D maps. I understand that its very routine but I had not any other alternatives. By the way during usage of the g_hbond with the below flags g_hbond -f fitted.trr -s complex.gro -n index.ndx -hbm ./hb/hbmap.xpm -life ./hb/hblife.xvg In the index file I've specified ligand and protein as two groups. should I define second group more accurately ( e.g only possible amino acids from the ligand binding pocket) ? I've forced with the problem of the interpretation of the hbmap. As I understood that could be used for the monitoring of the h-bond occurring and breaking between protein and ligand during MD run. How it could be visualize to observe particular amino-acids on the first (protein) group which contribute to H-bonds ? James 2013/4/24 Thomas Evangelidis teva...@gmail.com As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? fconv can do miracles :) check it out ! fconv -h In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ? In contrast, I encountered problems with the H-bonds VMD plugin, that's why I resorted to g_hbond. Beware that g_hbonds will count the frequencies of salt-bridges too. PoseView is used as the separate software or web server http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar interactions both in pymol as well as via pose view). If you find a way to draw the most important protein-ligand interactions throughout the trajectory with PoseView, then I would be very interested to know how. James 2013/4/24 Thomas Evangelidis teva...@gmail.com I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks? Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run. I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
[PyMOL] loadDir script
Dear PyMol users! I've forced with the problem of the loading of the my structural ensemble (pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into pymol via loadDir.pml script. In particular after loading of my ensemble in the right contex pymol's window I want to preserve structural order according to the pdb's names ( so that structures were listed in order from 1 to the 100.pdbs but not in the random (mixed) order). What additions to the loadDir script should I do to make such ordering ? James -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loadDir script
Thank you! Does it possible to include order *, yes to some pymol's setting file that the ordering be automatically each time when I load pdb ensemble? (I dont what to include it to the loadDir.pml script itself). James 2013/4/2 Thomas Holder thomas.hol...@schrodinger.com Hi James, please try, after loading the files: PyMOL order *, yes Cheers, Thomas James Starlight wrote, On 04/02/13 19:28: Pete, thanks for suggestion. I've tried to use loadDir with the pdb's subset where each file had name like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still wrong :( also is loadDir script I found block for c in glob( g ): cmd.load(c) if ( group != None ): cmd.group( group, basename(c).split(.)[0], add ) what should I change here to sort files correctly? James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Electrostatic potential surface
The problem with pdb2pqr have been solved :) Another question which I have is the calculation of the potential maps from the ensemble of the conformers (for example I want to compare potential distribution from the ensemble of the x-ray structures of one protein which were solved in different condition). In the visualization tab I found that APBS-2 can align maps. But what is the most suitable way to provide such ensemble for the calculations ? Should it be in NMR-like format or each conformer should be loaded by means of poadDir for instance ? How I can calculate maps from all conformers at once ? James 2013/3/28 James Starlight jmsstarli...@gmail.com by the way have someone had problems with the pdb2pqr usage with APBS in pymol? I've tried to install pdb2pqr from source as well as via packages then I've add usr/bin/pdb2pqr to the APBs plugin window and when I've started APBS I obtained error like Error: 5 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x333fcf8 (type: type 'function') Args: () Traceback (innermost last): File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1036, in execute good = self.generatePqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment If I launch pdb2pqr from the terminal I've obtained own@starlight ~/Desktop $ pdb2pqr Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH pdb2pqr.py: error: Incorrect number (0) of arguments! argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: [] should I provide some addition paths to the bash? James 2013/3/27 James Starlight jmsstarli...@gmail.com: As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charged groups. 2- What advantages has the usage of pdb2pqr plugin? Also in the pdb2pqr tools options I've found some options for force fields. As I know Poisson-Boltzmann equation on which APBS is based doesnt need any force fields (charge calculation from ab initio principles). Why force fields used here ? 3- IS there other plugins for the electrostatic surface calculation with (1) possibility to change cut-offs and (2) charge assignment from the force fields or ab initio calculations ? Thanks for help, James 2013/3/27 Mike Marchywka marchy...@hotmail.com: I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu
