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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