BTW using python script given by Matthew i've obtained error
>>> execfile ('pymol.py')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pymol.py", line 2, in <module>
import pymol
File "pymol.py", line 4, in <module>
pymol.finish_launching()
AttributeError: 'module' object has no attribute 'finish_launching'
it seems that pymol could not been imported (in my case it has been
installed by package manager and normally called from the command line)- so
to avoid such problems I have not to use python :)
James
2014-09-05 18:13 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> 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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