[Chimera-users] window size

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 6 17:55:33 PDT 2006

Hi Viktor,
You're welcome!

Unfortunately, although there is a large overlap between menu  
operations and commands, there is not a 1-to-1 relationship, and  
sometimes the mapping is not obvious. Some things can only be done in  
menus or GUIs, some only with commands. A brief historical perspective:  
  as Chimera was created, many commands from Midas were reimplemented in  
the new framework. Midas was almost completely command-driven.  As  
Chimera has been developed further, the Select and Actions menus and  
many new tools with complex GUIs have been added. Some but not all of  
these new tools have also been implemented as new commands.

The command
will hide all the atoms and bonds, but there is no command for changing  
to the orthographic projection.

If you (and other users out there) need particular operations to be  
available as commands, let us know, and that will be factored in as we  
set priorities.

Here are some ideas for figuring out correspondences, in order of  
decreasing efficiency (in my opinion):

(a) see the Chimera Commands Index

or the Chimera Quick Reference (PDF file)

which give brief explanations of what each command does; then you can  
look at the detailed man page for a command if it sounds like what you  

(b) There is some degree of cross-referencing in the User's Guide; for  
example, the Actions menu listing includes several "see also command"  

The two beginner tutorials go through mostly the same tasks, one using  
the menu, the other using commands.  However, it sounds like you are  
beyond the beginner stage, and it might not be convenient to put up the  
two tutorials in side-by-side browser windows.

(c) you can search for topics of interest with Help... Search  
Documentation. The hits will generally include some command man pages.

I hope this helps,

On Oct 6, 2006, at 2:00 PM, Viktor Hornak wrote:

> Hi Elaine,
> this is exactly what I needed. Also, thanks for a pointer to
> experimental features page (it's nice!).
> One other vaguely related question I had was whether it's possible to
> find out what chimera commands correspond to actions picked from menus
> or panels (e.g. Actions->Atoms/Bonds->Hide; Camera -> orthographic from
> Viewing/Side View panel, etc.). My objective is to capture everything I
> do in a specific session in chimera command scripts, which have an
> advantage over saving the session in that 1) I see what I did directly
> in the script, 2) these scripts are much smaller than session files.
> Thanks for your help!
> -Viktor
> Elaine Meng wrote:
>> Hi Viktor,
>> From our experimental features page
>> http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
>> you can download a "set magnification and window size" feature that
>> includes a "windowsize" command.
>> A related feature (unfortunately broken in past releases, but will be
>> available in the next release) is the --geometry startup option.  We
>> plan to make a release this month.  The --geometry option is not quite
>> as straightforward as the windowsize command, because depending on the
>> system, the specified size might include some of the bars around the
>> graphics window.  However, that just means you need to try it once,
>> use the "get pixels" button on the image-saving panel (File... Save
>> Image) to determine the actual graphics window dimensions, and at the
>> next startup use --geometry with the necessary additions or
>> subtractions to achieve the target size.  That's what I've been doing.
>> Startup options are described here:
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html
>> However, if you are on a Windows system, it is not very convenient to
>> use startup options (one way is to make a separate Chimera shortcut
>> and modify its properties). If you are on Windows, getting the
>> "windowsize" command from the experimental features page may be the
>> way to go.
>> I hope this helps,
>> Elaine
>> On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote:
>>> Dear All,
>>> I was wondering if there's chimera command that sets the size of  
>>> chimera
>>> window. Basically I just want to have a well defined window size  
>>> when I
>>> save pictures (or movies)...
>>> Thanks,
>>> -Viktor
>>> -- 
>>> Viktor Hornak
>>> SUNY at Stony Brook
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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