Re: [PyMOL] Memory not released after load and delete of structure
The suspension of undo doesn't have any effect on my accumulation of GB when working with Hybrid PyMol... Gianluigi Da: Thomas Holder thomas.hol...@schrodinger.com A: pymol-users@lists.sourceforge.net Inviato: Venerdì 21 Dicembre 2012 17:31 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Hi Gianluigi and Martin, thanks for reporting, this is a serious issue and we are looking into it. As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: cmd.set(suspend_undo, 1) Cheers, Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano chimic...@yahoo.it wrote: I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: Martin Hediger ma@bluewin.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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-- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412___ 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
[PyMOL] Renumber Script problem
Hi All, I've been having a bit of trouble recently with the renumber script. I have a pdb file that I'm trying to renumber, but unlike the other times I've used it, it is renumbering incorrectly. The numbers are usually spaced out 5 residues apart, but I have one number right near the beginning that is 6 residues down from the previous one. Needless to say, this is screwing up the rest of the count. Is there any idea why? I've provided a screenshot. Thanks, Alex attachment: renumbererror.png-- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412___ 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] Renumber Script problem
Does it have to be a pymol script. Renumbering pdbs is the bread and butter of
biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = %prog input.pdb output.pdb
parser= OptionParser(usage)
parser.add_option(-n,dest=start,help=residue number to start with,
default is 1,default=1)
parser.add_option(--preserve,dest=preserve,help=preserve insertion
code and heteroflags,default=False, action=store_true)
parser.add_option(--norestart,dest=norestart,help=don't start
renumbering at each chain, default=False,default=False, action=store_true)
(options, args) = parser.parse_args()
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
PDBparse = PDBParser(PERMISSIVE=1)
struct = PDBparse.get_structure(args[0][0:3],args[0])
residue_id = int(options.start)
chain_id =
for residue in struct.get_residues():
chain = residue.get_parent()
if(chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id=int(options.start)
if(options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
residue.id=(hetero,residue_id,insert)
else:
residue.id=(' ',residue_id,' ')
residue_id +=1
io=PDBIO()
io.set_structure(struct)
io.save(args[1])
if __name__ == __main__:
main()
Jordan
On Jan 21, 2013, at 12:21 PM, Alex Truong atru...@bu.edu wrote:
Hi All,
I've been having a bit of trouble recently with the renumber script. I have a
pdb file that I'm trying to renumber, but unlike the other times I've used
it, it is renumbering incorrectly. The numbers are usually spaced out 5
residues apart, but I have one number right near the beginning that is 6
residues down from the previous one. Needless to say, this is screwing up the
rest of the count. Is there any idea why? I've provided a screenshot.
Thanks,
Alex
renumbererror.png--
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Re: [PyMOL] Renumber Script problem
Hi Alex, the renumber script only sets the residue number, it does not reorder atoms internally. Just type PyMOL sort to sort internally based on the new residue numbers. See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Alex Truong wrote, On 01/21/13 19:21: Hi All, I've been having a bit of trouble recently with the renumber script. I have a pdb file that I'm trying to renumber, but unlike the other times I've used it, it is renumbering incorrectly. The numbers are usually spaced out 5 residues apart, but I have one number right near the beginning that is 6 residues down from the previous one. Needless to say, this is screwing up the rest of the count. Is there any idea why? I've provided a screenshot. Thanks, Alex -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ 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] Renumber Script problem
Hi Jordan,
nice script, but it does not do the same like the renumber script from
the PyMOLWiki (http://pymolwiki.org/index.php/Renumber). Try this: set
all residue numbers to 1, the renumber script will not care because it
walks along the bonds and increases the count whenever it passes a
peptide bond. The Biopython parser however will read just one residue.
Cheers,
Thomas
Jordan Willis wrote, On 01/21/13 19:53:
Does it have to be a pymol script. Renumbering pdbs is the bread and butter
of biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = %prog input.pdb output.pdb
parser= OptionParser(usage)
parser.add_option(-n,dest=start,help=residue number to start with,
default is 1,default=1)
parser.add_option(--preserve,dest=preserve,help=preserve insertion
code and heteroflags,default=False, action=store_true)
parser.add_option(--norestart,dest=norestart,help=don't start
renumbering at each chain, default=False,default=False, action=store_true)
(options, args) = parser.parse_args()
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
PDBparse = PDBParser(PERMISSIVE=1)
struct = PDBparse.get_structure(args[0][0:3],args[0])
residue_id = int(options.start)
chain_id =
for residue in struct.get_residues():
chain = residue.get_parent()
if(chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id=int(options.start)
if(options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
residue.id=(hetero,residue_id,insert)
else:
residue.id=(' ',residue_id,' ')
residue_id +=1
io=PDBIO()
io.set_structure(struct)
io.save(args[1])
if __name__ == __main__:
main()
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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