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.
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('${pdb}')
> cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
Alternatively,
I have got it, it works now!
in my example the double quotes were not escaped in pymol script :-)
the only (more python-oriented) question, would it be possible to
indicate chains_array for all letters A-Z (e.g. using some python
regex, rather just for A and B, chains_array = ["A", "B"], like in m
I actually tried to do like that still defining chains_array = ["A",
"B"] inside of pymol script and use external bash loop to loop over
pdbs
but it does not works ;(
#!/bin/bash
# this script rename chains in pdb to "empty" chain
home=$(pwd)
pdb_folder=$home/pdbs
output=$home/output
rm -r $output
yes, actually it is better because we avoid looping!
and how it would be possible to use array provided in the externall shell?
#!/bin/bash
pdb="final.pdb"
output=$(pwd)
# array given in bash
chains_array=('A' 'B')
# chains are cutted by pymol
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('chain '
If you want to rename multiple chains at once, make a selection like (chain
A+B+C). This list selection syntax is documented here:
https://pymolwiki.org/index.php/Property_Selectors
cmd.load(pdb)
cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
cmd.save('output.pdb')
Cheers,
Thomas
in python version I have got it
# to be run with PyMOL:
#pymol -ckqr pymol_cut_off.py
cut_off.py #
from pymol import cmd
pdb = "final.pdb"
chains_array = ["A", "B"] # two chains will be cuted
for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=
OK Lorenzo, thank you !
As an alternative question, would it be possible to put that loop
while renaming of the chains in the processed PBD within the bash
loop?
Here is an idea
#!/bin/bash
# this script rename chains in pdb to "empty" chain
pdb="my.pdb"
output=$(pwd)
# chain array is provided
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 t
Hi James,
not sure if it's relevant in this case, but you might also want to use
retain_order, to avoid messing up your pdbs.
https://pymolwiki.org/index.php/Retain_order
Cheers,
Lorenzo
Il giorno mar 25 giu 2019 alle ore 16:04 Thomas Holder <
thomas.hol...@schrodinger.com> ha scritto:
> > gene
Dear pymol users,
What is the purpose of the `selection` argument in the `load_traj` command?
My intuition would say that it allows to somehow select which atoms to load
into pymol before the actual loading happens. However, it seems to do
nothing whatsoever. What am I missing?
Thanks,
Lorenzo
_
> 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
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=\"\"')
c
Dear Mr. Thomas Holder,
Thank you very much for your kind reply.
I am very happy to know the scale factor for the 50% probability, but I
don't understand well.
>From the table, can I take a value the scale? For example, in case of 30%
probability, is it ok to set " set sphere_scale, 1.1932"? or n
Hi Koji,
Interesting question, I wasn't aware of the ellipsoid_probability setting.
The probability to radius conversion is done with a lookup table, see:
https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114
To get sphere scaling equivalent of ellipsoid_p
Hi James,
pdb_use_ter_records works in PyMOL 2.3.0, but not in previous versions (was
broken and then removed). See
https://pymolwiki.org/index.php/pdb_use_ter_records
Cheers,
Thomas
> On Jun 25, 2019, at 10:25 AM, James Starlight wrote:
>
> Dear Pymol Users!
>
> I need to process input P
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
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
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