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.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 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 <mailto: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
>>>>> <mailto: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
>>>>> <mailto: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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