Thanks Tsjerk!
Today I've tried some software of pairs alignment (like ce, tmalign and
mammoth) and found that it's not good for me because the positions of
reference and target are both altered as the result of the alignment by
means of the rotational matrix superimposition method. In my case I need to
move completely atoms of ref.pdb to the tar.pdb positions (whats pymol's
super command is actual do!) because I need to copy some docking
parameters (like docking box xyz vectors) from ref to each of the target.
So I'd be very thankful if someone shown me most trivial case to use super
command from the Pymol from the terminal in a few-line method (I really
wiuld like to avoid some python scripts from my bash) like:
load ref.pdb tar.pdb
super tar.pdb ref.pdb
save tar.pdb
Thanks for help,
James
2014-09-05 13:36 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hi James,
>
> I have a light version for fitting gromacs' gro files. No time to adapt
> that now for PDB, but it's not too hard.
>
> ./qfit.py source.gro target.gro > output.gro
>
> Hope it helps,
>
> Tsjerk
>
>
> On Fri, Sep 5, 2014 at 12:31 PM, James Starlight <jmsstarli...@gmail.com>
> wrote:
>
>> 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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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
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