Re: [PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU
Hi Jason ,
Thanks for your email.
I tried this with script with around 50 pdbs - that would be around 200
objects in the final session present in 50 groups.
The proteins are all in the 14-18 kDa range and monomeric.
My async_builds is off
My auto_defer_builds is set at 500
I used two versions :
1.5.0.3 on Windows XP 64 bit
with Quadro FX 880M
And
1.4.1 on a 64 bit Ubuntu Machine
With Quadro FX 3700
On both versions and machines I had the same behavior.
The Interesting thing is that, in the final session rotation is very
smooth ..and all the object seem to be loaded and responding fine. Its only
that most of the objects dont seem to be encompassed by all..So hiding
everything is not possible in this session rendering the session very
cluttered and the groups un-useable. Any idea what else may be affecting
my session.
Thanks
Hari
On Thu, Mar 15, 2012 at 11:13 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Hari,
I've tried your script on hundreds of objects and it seems to work
fine for me. What version of PyMOL are you using?
Do you have the async_builds setting on? If so, set to what value?
What about the auto_defer_builds settings?
I wonder if your video card is out of memory.
Cheers,
-- Jason
On Fri, Mar 9, 2012 at 5:59 PM, hari jayaram hari...@gmail.com wrote:
Hi I am scripting a visualization that involves roughly thirty to fifty
PDB
files with four objects each i.e 120 to 150 objects. I have a 64 bit
machine with 16 GB RAM and a Quadro FX 3700 card running Ubuntu Lucid.
At the end of the script I get a menu with what seems like all of the
objects suitably processed and grouped.
After this when I click all and say hide..everything , a whole lot of
objects still stay displayed . Getting the ids for some of them by right
clicking , it seems like they are not being included on the internal GUI
menu even when I scroll to the bottom.
These objects are clearly created by my script but it seems like they are
not part of all
Is it that all is not representing all of my objects because of some
limit
to number of objects that I am handling. The interesting thing is that
even
when all the objects are loaded Pymol remains very performant.
Here is my script...nothing fancy but just a loader and a grouper of PDBs
from a directory.
Any help will be greatly appreciated
Thanks
Hari
import cmd
import os
import pymol
import re
cpi = re.compile((\d{6}))
pymol.finish_launching()
for root,dirs,files in os.walk(/home/hari/mydownloadedPDbs/):
for afile in files:
print FILE,afile
if pdb in afile:
try:
cmd.load(os.path.join(root,afile))
except:
print Problem Loading:, afile
groups = []
for i in cmd.get_names():
try:
group_pool = []
surfdonor = surfdonor-%s % i[:10]
surfname = surf-%s % i[:10]
cartoon_object = cartoon-%s % i[:10]
ligands = ligands-%s % i[:10]
solvent = solvent-%s %i[:10]
# Create Object for surface and cartoon
cmd.copy(surfdonor,i)
cmd.copy(cartoon_object,i)
# Create selection containing ligands and make them into their
own
object
cmd.select(ligands+sel,organic and + surfdonor)
cmd.create(ligands,(%s)%ligands)
cmd.delete(ligands+sel)
group_pool.append(ligands)
# Create selection containing solvent
cmd.select(solvent+sel,resn HOH and + surfdonor)
cmd.create(solvent,(%s) % solvent)
cmd.delete(solvent+sel)
group_pool.append(solvent)
# Extract ligand object and solvent from surface clone object
cmd.extract(surfname,%s and not (resn HOH or organic) %
surfdonor)
cmd.delete(surfdonor)
group_pool.append(surfname)
pymol.preset.ligand_cartoon(cartoon_object)
group_pool.append(cartoon_object)
group_pool.append(cartoon_object + _pol_conts)
group_pool.append(i)
try:
group_name = %s%s % (str(i[0:3]),cpi.search(i).groups()[0])
except AttributeError:
group_name = group+ i
print group_name
cmd.group(group_name, .join(group_pool))
except :
print Problem with , i
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[PyMOL] AttributeError: 'module' object has no attribute 'super'
AttributeError: 'module' object has no attribute 'super' I am trying to run color_by_mutation http://www.pymolwiki.org/index.php/Color_By_Mutations But I get that error. Maybe my version of Mac PyMol from 2006 doesn't have that superimpose command? How do I fix this? Thank you. Shane -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] AttributeError: 'module' object has no attribute 'super'
Hi Shane, if you have a version 0.99 or older then there is no super command. That old version also lacks other features which are required by that script. So the only solution is to upgrade. Cheers, Thomas On 03/15/2012 05:47 PM, Shane Neeley wrote: AttributeError: 'module' object has no attribute 'super' I am trying to run color_by_mutation http://www.pymolwiki.org/index.php/Color_By_Mutations But I get that error. Maybe my version of Mac PyMol from 2006 doesn't have that superimpose command? How do I fix this? Thank you. Shane -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] fink install pymol help
Try fink install pymol-py27 From: Shane Neeley shane.nee...@gmail.com To: pymol-users@lists.sourceforge.net Sent: Thursday, March 15, 2012 4:53 PM Subject: [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get pymol install But it did not work. Do you know how I could install it with fink? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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-- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] fink install pymol help
Thanks Guys I just had to self update fink. On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley shane.nee...@gmail.comwrote: Hi, S.S. Thanks for your help. It says, Failed: no package found for specification 'pymol-py27'! null-b88d121ba616:~ chimpsarehungry$ fink list pymol Information about 312 packages read in 1 seconds. null-b88d121ba616:~ chimpsarehungry$ It doesn't appear to be a package available to me. On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj raj_...@yahoo.comwrote: Try fink install pymol-py27 -- *From:* Shane Neeley shane.nee...@gmail.com *To:* pymol-users@lists.sourceforge.net *Sent:* Thursday, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get *pymol install* * * But it did not work. Do you know how I could install it with fink? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] fink install pymol help
I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? On Thu, Mar 15, 2012 at 5:28 PM, Shane Neeley shane.nee...@gmail.comwrote: Thanks Guys I just had to self update fink. On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley shane.nee...@gmail.comwrote: Hi, S.S. Thanks for your help. It says, Failed: no package found for specification 'pymol-py27'! null-b88d121ba616:~ chimpsarehungry$ fink list pymol Information about 312 packages read in 1 seconds. null-b88d121ba616:~ chimpsarehungry$ It doesn't appear to be a package available to me. On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj raj_...@yahoo.com wrote: Try fink install pymol-py27 -- *From:* Shane Neeley shane.nee...@gmail.com *To:* pymol-users@lists.sourceforge.net *Sent:* Thursday, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get *pymol install* * * But it did not work. Do you know how I could install it with fink? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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
