Hi Thomas, thanks for the feedback.
I would like to point out that I observe this with version PyMOL 1.3
(also Hybrid), where, correct me if I'm wrong, there is no undo feature
available (at least I have never used or seen it here). To me this would
mean, the problem has to be with something else (possibly in addition to
undo).
To perfectly reproduce my situation, you can run the script that I
posted on pastebin (http://pastebin.com/mC6Rs6wk). Let me know if you
need some guidance with all the variables, I'm sorry for the terrible
code. I can also send you the PDB file I used when I got into this
problem, then you dont need to adjust any variables.
Best regards
Martin
On 21.12.12 17:31, Thomas Holder wrote:
> 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
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