Re: [PyMOL] refresh molecule display in python script

[Андрей Г. <gon...@gm...>]

So I've tryed to use cmd.refresh() and it has worked!

So your script must include the following:
cmd.load
cmd.refresh
[some actions]
cmd.load
cmd.refresh
[some actions]
etc.

2011/9/14 Matthias Schmidt <mat...@gm...>:
> Hi, not quite the script does the following:
>
> 1: load a file
> 2: modifiy this file using gromacs/editconf (because the cmd.rotate
> command is buggy) and os.system() calls
> 3: load the modified file
> 4: run some other external os.system() calls
>
> I would like to see the modified file before I run the other scripts
> in 4), but I can't because pymol will only update the open GL display
> once the script terminates.
>
> Matthias
>
> On Wed, Sep 14, 2011 at 3:00 PM, Андрей Гончар <gon...@gm...> wrote:
>> So what exactly do you want your script to do?
>> 1. Show loaded file
>> 2. Modify file
>> 3. Show modified file
>>
>> Is it right?
>>
>> 2011/9/14 Matthias Schmidt <mat...@gm...>:
>>> Hi,
>>>
>>> This approach does not work, because file.pdb is written in "do something..."
>>>
>>> Also, if I say "spawn script.py gloabl" instead of "run script.py",
>>> followed by script("parameter1", "...")
>>>
>>> the openGL display still won't refresh?
>>>
>>> Best,
>>>
>>> Matthias
>>>
>>> On Wed, Sep 14, 2011 at 1:59 PM, Андрей Гончар <gon...@gm...> wrote:
>>>> Try to do the following:
>>>> in your script.py
>>>>
>>>> from pymol import cmd
>>>>
>>>> cmd.load("file.pdb")
>>>>
>>>> def script():
>>>> do something...
>>>>
>>>> cmd.extend("script", script)
>>>>
>>>> In this case your pdb will be loaded before the script completes.
>>>>
>>>> 2011/9/14 Thomas Holder <sp...@us...>:
>>>>> Hi Matthias,
>>>>>
>>>>> use "spawn" instead of "run".
>>>>>
>>>>> http://pymolwiki.org/index.php/Fork
>>>>>
>>>>> Cheers,
>>>>>   Thomas
>>>>>
>>>>> On 09/14/2011 02:30 PM, Matthias Schmidt wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I am loading a pdb file in a python script for pymol.
>>>>>>
>>>>>> The script has the following structure:
>>>>>>
>>>>>> def script
>>>>>> do something
>>>>>> cmd.load("file.pdb")
>>>>>> do lot more
>>>>>> cmd.extend("script", script)
>>>>>>
>>>>>>   When the python script is completed,  the molecule file.pdb is shown
>>>>>> in the openGL display, but not before. How can I show the molecule
>>>>>> file.pdb in the display immediately after loading it and before "do
>>>>>> lot more" is executed?
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Matthias
>>>>>> --
>>>>>> Structural Bioinformatics and Computational Biochemistry Unit
>>>>>> Dept. of Biochemistry
>>>>>> University of Oxford
>>>>>>
>>>>>> http://sbcb.bioch.ox.ac.uk/schmidt.php
>>>>>
>>>>> --
>>>>> Thomas Holder
>>>>> MPI for Developmental Biology
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Андрей Гончар
>>>>
>>>> ------------------------------------------------------------------------------
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>>>> Learn about the latest advances in developing for the
>>>> BlackBerry&reg; mobile platform with sessions, labs & more.
>>>> See new tools and technologies. Register for BlackBerry&reg; DevCon today!
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>>>
>>>
>>>
>>> --
>>> Best,
>>>
>>> Matthias
>>> --
>>> Structural Bioinformatics and Computational Biochemistry Unit
>>> Dept. of Biochemistry
>>> University of Oxford
>>>
>>> http://sbcb.bioch.ox.ac.uk/schmidt.php
>>>
>>
>>
>>
>> --
>>
>> Андрей Гончар
>>
>> ------------------------------------------------------------------------------
>> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
>> Learn about the latest advances in developing for the
>> BlackBerry&reg; mobile platform with sessions, labs & more.
>> See new tools and technologies. Register for BlackBerry&reg; DevCon today!
>> http://p.sf.net/sfu/rim-devcon-copy1
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Best,
>
> Matthias
> --
> Structural Bioinformatics and Computational Biochemistry Unit
> Dept. of Biochemistry
> University of Oxford
>
> http://sbcb.bioch.ox.ac.uk/schmidt.php
>



-- 

Андрей Гончар