[Chimera-users] pymol get_view and set_view in Chimera?

Jan Kosinski kosinski at embl.de
Tue Feb 10 09:05:03 PST 2015


OK, I stay with using scripts in combination with sessions then!

Thanks for your always super fast response :-)
Jan

On 02/10/2015 06:00 PM, Elaine Meng wrote:
> Ah, I see.  I normally create a script but also save the session to be used along with the script.
>
> In that case, there is no equivalent.  Although there are Chimera commands to set scale, clipping plane positions, etc. they are all for relative changes rather than to some absolute value.  Sorry about that,
> Elaine
>
> On Feb 10, 2015, at 8:53 AM, Jan Kosinski <kosinski at embl.de> wrote:
>
>> Dear Elaine,
>>
>> I would like to be able to copy the position info to a chimera script rather than a session. With set_view/get_view it is possible. The one can write a script that sets window size, set view, load structures, change appearance, and render a figure. If one needs to change a file from which model is loaded, with script it involves quick edit of a text file.
>>
>> I seek for that just for convenience of having everything in one editable script rather than keeping a session with saved positions.
>>
>> Best,
>> Jan
>>
>> On 02/10/2015 05:21 PM, Elaine Meng wrote:
>>> Dear Jan,
>>> I believe "savepos" and "reset" are the Chimera equivalents, e.g.
>>>
>>> savepos name1
>>> [...move stuff around...]
>>> savepos name2
>>> reset name1
>>> reset name2 80
>>>
>>> What savepos saves sounds like the same stuff as in the pymol setview description, not sure why you rejected it as the equivalent:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>
>>>
>>> Chimera also allows saving/restoring scenes, which besides the position information also include display styles, colors, etc.  See the "scene" command:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scene.html>
>>>
>>> Because scenes contain more information than positions, they can make Chimera session files rather large.
>>> I hope this helps,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>
>>> On Feb 10, 2015, at 7:19 AM, Jan Kosinski <kosinski at embl.de> wrote:
>>>
>>>> Is there an equivalent of pymol get_view and set_view in Chimera?
>>>>
>>>> I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View), which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View).
>>>>
>>>> Thanks in advance,
>>>> Jan
>>>>
>>
>> -- 
>> Jan Kosinski, PhD
>> Structural and Computational Biology Unit
>> European Molecular Biology Laboratory (EMBL)
>> Meyerhofstrasse 1
>> 69117 Heidelberg
>> Germany
>>
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-- 
Jan Kosinski, PhD
Structural and Computational Biology Unit
European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1
69117 Heidelberg
Germany



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