[Chimera-users] command line zone selection?

Kenward Vaughan kvaughan at bc.cc.ca.us
Sat Dec 30 19:14:02 PST 2006

On Saturday 30 December 2006 14:29, Elaine Meng wrote:
> 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.

> 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.

I have uncovered the "problem."  In one panel, I might have the 

	roll y 1 22 ; roll x -0.8182 22

and in the following panel:

	repre stick ; color byatom

This causes the view in the second panel to revert to what existed prior 
to the first.  **This happens regardless of how long one waits before 
moving forward from one panel to the next.  It is independent of any 
manual manipulation as well.**

If the first line is terminated with a wait:

	roll y 1 22 ; roll x -0.8182 22 ; wait

then the view generated by the rolls is maintained.

I took the COX inhibitor demo and tested this with several lines in 
there as well (7-10, IIRC). The results matched what I see with my own. 
I've attached two small jpg's which show the effect of removing the 
wait found in panel 9. 

I had understood from the help files that "wait" insured following 
commands were not processed until molecular motion had stopped.  I had 
not included it in my lines since I knew that it wouldn't be needed 
(the rolls were the only commands processed before control was 
relinquished back to the user).

Apparently the "wait" is required to properly set the coordinates for 
the next panel.

> About specifying a bunch of atoms over and over, you can name a
> selection and then use the selection's name. See
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#namesel
> 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)

It's definitely a good start!  Thanks!

> Technically we aren't working today.  However, I like to check my
> mail every day and will occasionally answer mail from devoted Chimera
> users! 8-)
> I hope this helps,
> Elaine

Happy New Year!  :-)


> 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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