Hi James,
adding my 2 cents to this conversation. Save the bash script below as
"pymolsuper.sh".
----------------- pymolsuper.sh ---------------------
#!/bin/bash
if [[ $# < 2 ]]; then
echo "usage: $0 mobile.pdb target.pdb [out.pdb]"
exit 1
fi
script="python
names = cmd.get_object_list()
cmd.super(names[0], names[1])
cmd.save(sys.argv[1] or 'out.pdb', names[0])
python end"
pymol -cqk "$1" "$2" -d "$script" -- "$3"
---------------------------------------------------------
Hope that helps.
Cheers,
Thomas
On 05 Sep 2014, at 12:13, James Starlight <jmsstarli...@gmail.com> wrote:
> 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
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
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