[Chimera-users] vop morph map color

Henning Stahlberg henning.stahlberg at unibas.ch
Thu Feb 28 12:41:17 PST 2013

Is it possible to generate a morphing between two volumes in Chimera, if the volumes have slighly different sizes, e.g. 100x100x100 vs. 101x101x101 pixels?  Can I crop or pad a volume in Chimera?


On Feb 28, 2013, at 6:25 PM, Elaine Meng wrote:

> Hi Steve,
> To avoid displaying intermediate states, you can combine commands on one line with semicolon separators, for example:
> vop morph #0,1; volume #2 color khaki
> See the general information on command files:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
> Another possibility in this case is to create the morph volume, color it as desired, and hide it before starting recording (before the "movie record" command), and just redisplay it later in the movie content portion of the script.
> 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 28, 2013, at 8:20 AM, Steve Reichow wrote:
>> Hi, 
>> I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1:
>> vop morph #0,1
>> The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following:
>> vop morph #0,1
>> volume #2 color khaki
>> This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
>> I am using Chimera Version 1.6 Mac OSX
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