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
On Thu, Sep 4, 2014 at 6:19 AM, James Starlight
<jmsstarli...@gmail.com <mailto:jmsstarli...@gmail.com>>
wrote:
Hi Tsjerk,
Thanks alot!
Also I have the task to merge protein.pdb and
lipids.pdb with some 1 line shell command ( like CAT)
to obtain protein inserted in the lipids (the seccond
file is consist of the whole which can locate the
protein). My problem is that both protein.pdb and
lipids.pdb consisted of the unusuall first line which
should be deleated before it merging (in my case it's
the HEADER lala.pdb). could you suggest me the
combination of grep sed command which should be used
to deleate the first line from both pdbs and than
merge it in one-command method?
Many thanks,
James
2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar
<tsje...@gmail.com <mailto:tsje...@gmail.com>>:
Hi James,
You can use pymol -cd "pymolcommands". See
http://www.pymolwiki.org/index.php/Command_Line_Options
However, the first part is much easier with grep
or sed. To remove all solvent molecules:
grep -v "^ATOM.*SOL" in.pdb > out.pdb
To remove NA+/CL- too
grep -v "ATOM.*\(SOL\|NA+\|CL-\)" in.pdb > out.pdb
The fitting is a bit more cumbersome :)
Hope it helps,
Tsjerk
On Thu, Sep 4, 2014 at 10:19 AM, James Starlight
<jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>> wrote:
Dear PyMol users!
I'd like to find possibilities for running of
some pymol commands from the terminal. For
instance in my case I' d like perform 2 simple
steps (both in terminal not in the pymol GUI)
to remove water and ions from my target input
pdb (typical I do it via gromacs editconf)
superimpose target.pdb against reference.pdb (
i do it by means of tmalign utility)
Thanks for help,
James
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