[PyMOL] Printing Protein Surface residues
Hi All I have a task in hand where need your suggestions and comments Task is to print list of solvent exposed surface amino acids or protein surface amino acids . By searching I had found this script http://www.pymolwiki.org/index.php/FindSurfaceResidues which select the residues on the surface but I dont know how to print the residues names as an output ? Thanks in advance ... -- Please feel free to call me or mail me Thanks and Regards Vinod.D M.Pharm. Jr. Applications Scientist Mobile no:+91-9900090044 http://www.schrodinger.com/ -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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] Printing Protein Surface residues
Hi Vinod The exposed residues are stored in the selection “exposed_res_02”. You can iterate http://www.pymolwiki.org/index.php/Iterate this selection to get several properties like the residues names, for example the command: iterate exposed_res_02, resn will return the name of the residues, and the command iterate exposed_res_02, resn, resi will return the name and the residue number. Cheers, Osvaldo. On Thu, May 21, 2015 at 7:03 AM, Vinod Devaraji vinod.devar...@schrodinger.com wrote: Hi All I have a task in hand where need your suggestions and comments Task is to print list of solvent exposed surface amino acids or protein surface amino acids . By searching I had found this script http://www.pymolwiki.org/index.php/FindSurfaceResidues which select the residues on the surface but I dont know how to print the residues names as an output ? Thanks in advance ... -- Please feel free to call me or mail me Thanks and Regards Vinod.D M.Pharm. Jr. Applications Scientist Mobile no:+91-9900090044 http://www.schrodinger.com/ -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ 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 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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] Printing Protein Surface residues
Hej,
depends on what you want, single atoms or residues. You can output the
available surface are for every atom and then decide which ones are
accessible based on your cutoff stringency.
Here is some code that will print the info in PyMOL, alternatively you
could modify it to print to a file instead, but copy-paste to EXCEL works
fine.
# Object list
objectlist=cmd.get_object_list()
# Calculate area:
python
cmd.set('dot_solvent',1)
for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
# this writes the area into the b-factor field
python end
# print info
print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
Then, in EXCEL you can use the data (sort/filter) to figure out which atoms
are most exposed, or above a set threshold.
Hope this is useful,
Andreas
On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji
vinod.devar...@schrodinger.com wrote:
Hi All
I have a task in hand where need your suggestions and comments
Task is to print list of solvent exposed surface amino acids or protein
surface amino acids .
By searching I had found this script
http://www.pymolwiki.org/index.php/FindSurfaceResidues
which select the residues on the surface but I dont know
how to print the residues names as an output ?
Thanks in advance ...
--
Please feel free to call me or mail me
Thanks and Regards
Vinod.D M.Pharm.
Jr. Applications Scientist
Mobile no:+91-9900090044
http://www.schrodinger.com/
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
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--
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Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
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