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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