[Chimera-users] command line zone selection?

Elaine Meng meng at cgl.ucsf.edu
Sat Dec 30 14:29:25 PST 2006

Hi Kenward,
Just changing the color or representation should not reset the 
orientation *achieved by commands* (more explanation below) at the end 
of the previous panel.  There are examples in the demos that come with 
Chimera (Tools... Demos) - e.g. in the hormone-receptor demo, the 
position does not reset to the original when switching from panel 2 to 
panel 3 (FSH undisplayed, leucines in FSH receptor displayed). I also 
tried playing this demo up to panel 2, opening the demo in the editor 
(from the Demo dialog, File... Open in Editor), unchecking the roll 
commands in panel 3, and then clicking Execute  to test whether having 
some movement suppresses a reset bug. However, there was still no reset 
between panels 2 and 3.  I'm using version 1.2304.

Note that any rotations/translations performed *manually* will not be 
incorporated into a panel, only the ones expressed as commands.  If you 
rotated/translated manually, there will be a resetting to the 
orientation without those manual movements before the next set of 
commands are applied.  Perhaps that is what happened. That is the 
tricky thing about Demos:  everything must be done with commands, and 
it can take a fair amount of effort to get the orientations you want.  
Actually, the resetting to the orientation achieved purely by commands 
is at least partly a feature rather than a bug, because it allows demo 
viewers to change the view manually within a panel however they desire 
without disrupting the views the demo creator intended to be visited 
during the course of the demo.  Hope that makes sense...  It may be 
instructive to open the existing demos in the editor as mentioned 
above, if you haven't tried that already.

If the problem persists, let me know what version of Chimera you're 
using.  Also, if you want you could send me your demo file and any 
associated data files and I could take a more in-depth look next week.

About specifying a bunch of atoms over and over, you can name a 
selection and then use the selection's name. See

However, a selection can only be named using the menu currently, so for 
Demos  a different approach is required. In similar situations, I 
bypass selection entirely and instead alias that set of atoms (using 
the same specifications that you would have used to select the atoms) 
and then use the resulting alias in subsequent commands. For example:

Command: alias key #0:17.a,138.a,190.a #1:38.b,158.b,221.b 
Command: rep sphere key
Command: focus key
Command: color byatom key

The alias statement can include all kinds of specifications - zones, 
categories such as "ligand," combination operators & | ~ , etc.   Man 
page for "alias":

Technically we aren't working today.  However, I like to check my mail 
every day and will occasionally answer mail from devoted Chimera users! 

I hope this helps,
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

On Dec 30, 2006, at 12:30 PM, Kenward Vaughan wrote:

> In my demo, I've found that rotating a model about to create a specific
> view in one panel, followed in the next panel by either changing the
> atom representation or recoloring the atoms, causes a resetting of the
> view to the opening orientation.  Is this a known issue?
> Kenward
> ps. BTW, can a selected group of atoms be named at the command line?
> Another question I can't seem to find an answer to... :(
> -- 
>                                        .'^~;,_
> Dr. Kenward Vaughan                    `:,'~~~~~
> Professor of Chemistry                 \;:/
> Bakersfield College                    |,;|
> 1801 Panorama Drive                   / ', \
> Bakersfield, CA  93305               / o  O \
> http://www2.bc.cc.ca.us/kvaughan    (oOoOOoOo)
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