Re: [PyMOL] Shell utilities for structural bioinformatics
From the previous task it's OK now
small question about pymol :)
how to prevent removing TER record after editing of the structure using
pymol
e.g I used the following command to load protein-ligand complex (where
there is TER between protein and ligand) and remove hydrogens and than save
back it to new pdb where there were no more TER records
pymol $pdb -c -q -d remove hydrogens; save
${temp}/${filenamenoextention}_noH.pdb, ${filenamenoextention}
${temp}/xz.log
and smth about shell informatics:
how to scan specified string in pdb corresponded to the last line of the
ligand (which is the RES in pdb) and add after this line TER record. E.g
the basic idea:
grep -v ATOM.*\(RES\|MOL\) $pdb | # smth with sed pdb_with_TER.pdb
now I only would like to know proper reg expression in my case for GREP and
command for SED
James
2014-09-24 11:06 GMT+02:00 James Starlight jmsstarli...@gmail.com:
some additional question about shell scripting (copied from the amber
forum because I'd like to find as more sollutions of this problem as
possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
fashion.
In my case I use tleap as part of some big script to process many
models.pdb for further md simulation. Each of the model consist of pair of
CYX residues (assigned by pdb2pqr) in different positions of its sequence.
So in script I need firstly to know the number of position for each of CYX
residues of each model and than to fill this numbers to the tleap input
files for each model
in bash for one model it will be look like:
#some command to scan the sequence of model.pdb and define pair of its CYX
residues within it as the k ans i variables
printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
protein protein.parm7 protein.inpcrd\nquit ./tleap.in
so my task is only to find some command which will scan model and find
positions of the CYX within its sequence which could be put to the tleap as
two digits. It will be better to find those 2 digits using pdb as an input
and some unix command like sed or grep to find positions
I will be very thankful for any suggestions!
James
2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log
man csplit:
csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
0\|^MODEL\|^REMARK | sed -e 's/^ENDMDL/TER/g' firstmodel.pdb
sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
0\|MODEL\|REMARK\)/d' my_docking.pdb firstmodel.pdb
... shorter and one process running in stead of 3.
Cheers,
Tsjerk
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Re: [PyMOL] Shell utilities for structural bioinformatics
some additional question about shell scripting (copied from the amber forum
because I'd like to find as more sollutions of this problem as possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
fashion.
In my case I use tleap as part of some big script to process many
models.pdb for further md simulation. Each of the model consist of pair of
CYX residues (assigned by pdb2pqr) in different positions of its sequence.
So in script I need firstly to know the number of position for each of CYX
residues of each model and than to fill this numbers to the tleap input
files for each model
in bash for one model it will be look like:
#some command to scan the sequence of model.pdb and define pair of its CYX
residues within it as the k ans i variables
printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
protein protein.parm7 protein.inpcrd\nquit ./tleap.in
so my task is only to find some command which will scan model and find
positions of the CYX within its sequence which could be put to the tleap as
two digits. It will be better to find those 2 digits using pdb as an input
and some unix command like sed or grep to find positions
I will be very thankful for any suggestions!
James
2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log
man csplit:
csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
0\|^MODEL\|^REMARK | sed -e 's/^ENDMDL/TER/g' firstmodel.pdb
sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
0\|MODEL\|REMARK\)/d' my_docking.pdb firstmodel.pdb
... shorter and one process running in stead of 3.
Cheers,
Tsjerk
--
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Re: [PyMOL] Shell utilities for structural bioinformatics
Hi, some new question. I need to some combination of shell utilities to split multi_model.pdb on several pdbs as well as separate command to seek multi_model.pdb and to save only this model as the separare model1.pdb. I've tried to do it using grep grep '^MODEL 1' my_docking.pdb model1.pdb but results were empty. James 2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com: Thanks you very much! James 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com: Hi Small correction to Gianlucas suggestion will direct the output to a file, overwriting the contents will direct the output to a file, appending the contents Venlig hilsen Folmer Fredslund Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr: Don't even need cat simply do grep PPC ref.pdb tar_i.pdb redirecting std out with appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
Hi James,
These are the sort of questions that'll be answered elsewhere. Most notably
on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b %04d.pdb file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb on
several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting the contents
will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've decided to open new topic focused on the implementation of the
common shell utilities like grep awk and sed for the structural
bioinformatics tasks like processing and editing of the large sets of
pdbs.
In my current task I need to copy all lipids from one pdb (called it
ref) to another call it tar_i.pdb (both files have the same 3D shape
and
have been superimposed before that): so in that case I guess lipids
could be recognized by residue name in pdb file (PPC) as well as by
its
#4 column number (what is actually do grep). So the algorithm might
be:
select from the ref.pdb all strings where #4 column is PPC and merge
it
(by means of CAT I guess) with the tar_i.pdb. Please show me some
example of the one-line method of this realization.
Thanks,
James
--
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--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
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Re: [PyMOL] Shell utilities for structural bioinformatics
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e,g in my case each model after spliting consist of
MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL
i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and change
ENDMDL to TER
i've tried to do it
csplit -b %04d.pdb my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' |
grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g'
but the resulted files still consist of unused lines
BTW might the csplit be used to extract only ONE (e,g first) model from the
multi-pdb file?
James
2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi James,
These are the sort of questions that'll be answered elsewhere. Most
notably on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b %04d.pdb file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb on
several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting the contents
will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr
:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've decided to open new topic focused on the implementation of the
common shell utilities like grep awk and sed for the structural
bioinformatics tasks like processing and editing of the large sets
of pdbs.
In my current task I need to copy all lipids from one pdb (called it
ref) to another call it tar_i.pdb (both files have the same 3D shape
and
have been superimposed before that): so in that case I guess lipids
could be recognized by residue name in pdb file (PPC) as well as by
its
#4 column number (what is actually do grep). So the algorithm might
be:
select from the ref.pdb all strings where #4 column is PPC and merge
it
(by means of CAT I guess) with the tar_i.pdb. Please show me some
example of the one-line method of this realization.
Thanks,
James
--
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--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
--
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Re: [PyMOL] Shell utilities for structural bioinformatics
Hi James,
This is more text-file processing than it is bioinformatics. The trick is
to understand the problem, dissect it, and fit it to your toolbox on Linux.
That's actually much of bioinformatics :)
The first thing to understand is what data you have and what data you need
to have in the end. That will determine the tools and how to use them. To
extract the first part of a file, up to and including a tag (ENDMDL), you
could use sed:
sed /^ENDMDL/q models.pdb firstmodel.pdb
While at it, you can also delete those lines you don't want to:
sed -e /^ROOT/d -e /^ENDROOT/d -e /^TORSDOF/d -e /^ENDMDL/q models.pdb
firstmodel.pdb
For bioinformatics, it really pays off to read up on sed and awk.
As for the other question, yes, csplit can be used to extract one, or a
number of blocks. The {*} indicates that all blocks are to be written. {10}
indicates the first ten blocks are to be written. Check the help to see how
to use csplit to extract a specific block. I just read up on it now to be
able to answer your question. I didn't know this about csplit when I woke
up this morning.
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 12:00 PM, James Starlight jmsstarli...@gmail.com
wrote:
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e,g in my case each model after spliting consist of
MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL
i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and change
ENDMDL to TER
i've tried to do it
csplit -b %04d.pdb my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' |
grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g'
but the resulted files still consist of unused lines
BTW might the csplit be used to extract only ONE (e,g first) model from
the multi-pdb file?
James
2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi James,
These are the sort of questions that'll be answered elsewhere. Most
notably on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b %04d.pdb file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb
on several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting the contents
will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr
:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've decided to open new topic focused on the implementation of the
common shell utilities like grep awk and sed for the structural
bioinformatics tasks like processing and editing of the large sets
of pdbs.
In my current task I need to copy all lipids from one pdb (called it
ref) to another call it tar_i.pdb (both files have the same 3D
shape and
have been superimposed before that): so in that case I guess lipids
could be recognized by residue name in pdb file (PPC) as well as by
its
#4 column number (what is actually do grep). So the algorithm
might be:
select from the ref.pdb all strings where #4 column is PPC and
merge it
(by means of CAT I guess) with the tar_i.pdb. Please show me some
example of the one-line method of this realization.
Thanks,
James
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
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--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
Re: [PyMOL] Shell utilities for structural bioinformatics
Hi James,
How about
egrep -v MODEL 1|ROOT|ATOMS|ENDROOT|TORSDOF myoriginalfile | sed
's/ENDMDL/TER/' mynewfile
-v in egrep is to reverse the selection so you get all lines except that
ones in the expression. Without that you _only_ grep the lines with
those expressions.
(egrep might be grep, or something similar depending on OS or variant of
it)
And sed (stream editor) then s(ubstitutes) ENDMDL with TER.
hth, Marko
On 12/09/2014 11:00, James Starlight wrote:
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to
ask it here some expert of this topic like you :)
because in my case I need to further proceed each split model model
(e,g delete some lines or make changing) piping with some commands
e,g in my case each model after spliting consist of
MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL
i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and
change ENDMDL to TER
i've tried to do it
csplit -b %04d.pdb my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT'
| grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g'
but the resulted files still consist of unused lines
BTW might the csplit be used to extract only ONE (e,g first) model
from the multi-pdb file?
James
2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com
mailto:tsje...@gmail.com:
Hi James,
These are the sort of questions that'll be answered elsewhere.
Most notably on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b %04d.pdb file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight
jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com wrote:
Hi,
some new question.
I need to some combination of shell utilities to split
multi_model.pdb on several pdbs as well as separate command
to seek multi_model.pdb and to save only this model as the
separare model1.pdb. I've tried to do it using grep
grep '^MODEL 1' my_docking.pdb model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight
jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund
folm...@gmail.com mailto:folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting the
contents
will direct the output to a file, appending the
contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev Gianluca Santoni
gianluca.sant...@ibs.fr
mailto:gianluca.sant...@ibs.fr:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to
the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've decided to open new topic focused on the
implementation of the
common shell utilities like grep awk and sed for
the structural
bioinformatics tasks like processing and editing
of the large sets of pdbs.
In my current task I need to copy all lipids
from one pdb (called it
ref) to another call it tar_i.pdb (both files
have the same 3D shape and
have been superimposed before that): so in that
case I guess lipids
could be recognized by residue name in pdb file
(PPC) as well as by its
#4 column number (what is actually do grep). So
the algorithm might be:
select from the ref.pdb all strings where #4
column is PPC and merge it
(by means of CAT I guess) with the tar_i.pdb.
Please show me some
example of the one-line method of this realization.
Thanks,
James
--
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Re: [PyMOL] Shell utilities for structural bioinformatics
Thank you very much! James 2014-09-12 12:36 GMT+02:00 Marko Hyvonen mh...@cam.ac.uk: On 12/09/2014 11:26, James Starlight wrote: grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK| I think you are missing few | in there: grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK and depending on the shell, you might be able get away with \ by using single quotation marks grep -v '^ROOT|^ENDROOT|^TORSDOF 0|^MODEL|^REMARK' Marko -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel:+44-(0)1223-766 044 -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log
man csplit:
csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
0\|^MODEL\|^REMARK | sed -e 's/^ENDMDL/TER/g' firstmodel.pdb
sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
0\|MODEL\|REMARK\)/d' my_docking.pdb firstmodel.pdb
... shorter and one process running in stead of 3.
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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Re: [PyMOL] Shell utilities for structural bioinformatics
Thanks you very much! James 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com: Hi Small correction to Gianlucas suggestion will direct the output to a file, overwriting the contents will direct the output to a file, appending the contents Venlig hilsen Folmer Fredslund Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr: Don't even need cat simply do grep PPC ref.pdb tar_i.pdb redirecting std out with appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shell utilities for structural bioinformatics
Don't even need cat simply do grep PPC ref.pdb tar_i.pdb redirecting std out with appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it ref) to another call it tar_i.pdb (both files have the same 3D shape and have been superimposed before that): so in that case I guess lipids could be recognized by residue name in pdb file (PPC) as well as by its #4 column number (what is actually do grep). So the algorithm might be: select from the ref.pdb all strings where #4 column is PPC and merge it (by means of CAT I guess) with the tar_i.pdb. Please show me some example of the one-line method of this realization. Thanks, James -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
