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.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>:
>>
>>> 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>:
>>>
>>>> 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
>>>>>>
>>>>>>
>
------------------------------------------------------------------------------
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
