Re: [PyMOL] Access to pymol commands from the terminal
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
# dock each model to the ligand
for pdb in $receptors/*.pdb; do
filename=$(basename $pdb)
M=${filename/.pdb/}
echo Processing of ${M} is initiated...
#remove water and ions; change EMD to TER
grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g'
${dirr}/temp/${M}_clean.pdb
#superimsoposition using pymol against reference
pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi
2-280; save ./superimposed/${M}_aligned.pdb, $M
./superimposed/pymol_${M}.log
cp $ref ./superimposed
done
two additional questions:
1) will it possible to use more flexibility in case of the selection of
region for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?
2) what advantages could give me tmalign method for the superimposition in
comparison to super and ce programs? does the coordinates of the reference
will not changed after alignment of each mobile on it (like fitting in case
of super) ?
James
2014-09-22 10:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
2014-09-19 20:19 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
I don’t have any experience with Profit. However, instead of using
something like” PyMOL’s `super` command as you asked, you could actually
use `super` in your shell session by launching PyMOL in command line mode
http://www.pymolwiki.org/index.php/Command_Line_Options. Of course,
you would need to modify it according to your file naming scheme, but
here’s a working example.
###
#!/bin/bash
REF=reference.pdb
# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
i=$((i+1))
done
mv mobile0.pdb $REF
# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')
# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
${M}_aligned.pdb
done
pymol mobile*_aligned.pdb
###
You could also use CEalign if you need something citable, just switch
the order of the arguments to it: `cealign $R and resi 1-110, $M`.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 19, 2014, at 6:03 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear all,
I still need some help regarding some algorithm for structural
superimposition of my mobile structures regarding one specified reference
using some fitting method (to avoid changing in the position of the
reference.pdb which is very important for me!)=something like super
command in pymol. Using ProFit I have faced with some errors during
superimposition regarding the chosing reference (in case where there were
some differences in the positions of ref and mob structures its alignment
was not perfect (the mob had not been fully aligned on the ref) obtaining
very big RMSD (20 A!) as the result although its actual value should be in
range of 2-5 A. I'll be thankful for possible sollutions of this problem
using Profit is there are users experienced with this software (mb it
should to define fitting zones or atom subsets more accurately but I have
no ideas here ) or any other alternatives which could be used as parts of
the shell script.
James
--
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Re: [PyMOL] Molecular Visualisation in PyMol
Hi Jed, so this method is working of the ensemble of the pdb files taken from the MD simulation or NMR structure, isnt it? Could someone explain me step by step how to obtain such inputs for the PyMol (from the step when I've load my trajectory to the VMD). James 2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu: You could extract the flexible residues into one multistate object and use show all_states. So, you'd only be dealing with 2 objects - Ca and residues. Jed On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/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 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/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] Molecular Visualisation in PyMol
I should to specify that I ask this because normally VMD didn't produce multi-state pdb from the md trajectory so it seems I need to use some plugin to load *.dcd or *.trr James 2014-09-22 13:53 GMT+04:00 James Starlight jmsstarli...@gmail.com: Hi Jed, so this method is working of the ensemble of the pdb files taken from the MD simulation or NMR structure, isnt it? Could someone explain me step by step how to obtain such inputs for the PyMol (from the step when I've load my trajectory to the VMD). James 2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu: You could extract the flexible residues into one multistate object and use show all_states. So, you'd only be dealing with 2 objects - Ca and residues. Jed On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! In this topic I've decide to put all questions regarding visualisation. This time I'm very intresting whether it possible to add some effect of the flexebility or ensemble-like dynamics on the selected elements (e.g selected side-chains to convey a sense of its flexibility like in the molecular dynamics simulation) by introdycing of some filter on this part like some kind of bluring). Of cource I can do it by taking several aligned snapshots from MD and load it in the Pymol but here I wounder if its also possible do from one pdb structure. Thanks for help, James -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/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 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/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] Access to pymol commands from the terminal
Hi James -
On Sep 22, 2014, at 4:30 AM, James Starlight
jmsstarli...@gmail.commailto:jmsstarli...@gmail.com wrote:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
# dock each model to the ligand
for pdb in $receptors/*.pdb; do
filename=$(basename $pdb)
M=${filename/.pdb/}
echo Processing of ${M} is initiated...
#remove water and ions; change EMD to TER
grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g'
${dirr}/temp/${M}_clean.pdb
#superimsoposition using pymol against reference
pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi 2-280;
save ./superimposed/${M}_aligned.pdb, $M ./superimposed/pymol_${M}.log
cp $ref ./superimposed
done
Glad it worked for you.
two additional questions:
1) will it possible to use more flexibility in case of the selection of region
for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?
Try `$R and resi 2-280 and ss h`. See
http://www.pymolwiki.org/index.php/Property_Selectors for more info. (That
page comes up as the very first result for me on Google with “pymol select
secondary structure” as the search term.)
2) what advantages could give me tmalign method for the superimposition in
comparison to super and ce programs? does the coordinates of the reference will
not changed after alignment of each mobile on it (like fitting in case of
super) ?
From the description here (http://www.pymolwiki.org/index.php/TMalign) that
TMalign, like CEalign, can be useful for structures in the “twilight zone,”
where sequence alignment by `align` or structural alignment by `super` may not
provide a good fit. For any of the programs, though, only the mobile
structures should move; the target/reference coordinates should always remain
unchanged.
Cheers,
Jared
James
2014-09-22 10:21 GMT+02:00 James Starlight
jmsstarli...@gmail.commailto:jmsstarli...@gmail.com:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
2014-09-19 20:19 GMT+02:00 Sampson, Jared
jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org:
Hi James -
I don’t have any experience with Profit. However, instead of using something
like” PyMOL’s `super` command as you asked, you could actually use `super` in
your shell session by launching PyMOL in command line
modehttp://www.pymolwiki.org/index.php/Command_Line_Options. Of course, you
would need to modify it according to your file naming scheme, but here’s a
working example.
###
#!/bin/bash
REF=reference.pdb
# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
i=$((i+1))
done
mv mobile0.pdb $REF
# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')
# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
${M}_aligned.pdb
done
pymol mobile*_aligned.pdb
###
You could also use CEalign if you need something citable, just switch the order
of the arguments to it: `cealign $R and resi 1-110, $M`.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 19, 2014, at 6:03 AM, James Starlight
jmsstarli...@gmail.commailto:jmsstarli...@gmail.com wrote:
Dear all,
I still need some help regarding some algorithm for structural superimposition
of my mobile structures regarding one specified reference using some fitting
method (to avoid changing in the position of the reference.pdb which is very
important for me!)=something like super command in pymol. Using ProFit I have
faced with some errors during superimposition regarding the chosing reference
(in case where there were some differences in the positions of ref and mob
structures its alignment was not perfect (the mob had not been fully aligned on
the ref) obtaining very big RMSD (20 A!) as the result although its actual
value should be in range of 2-5 A. I'll be thankful for possible sollutions of
this problem using Profit is there are users experienced with this software (mb
it should to define fitting zones or atom subsets more accurately but I have no
ideas here ) or any other alternatives which could be used as parts of the
shell script.
James
--
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Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download
