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.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
>>>>>>>
>>>>>>>
>>
>
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