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
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