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
<mailto: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
<mailto: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 <mailto: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 <mailto: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 <mailto: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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