[Chimera-users] vop morph map color

[Tom Goddard]

Hi Henning,

  Morph map just does a linear interpolation between corresponding map grid points and it requires the map sizes be the same.  Also the grids of the two maps should exactly match if you want sensible results.  If your maps are different sizes or the same size but the grids are not aligned you would use the "vop resample" command to interpolate one map on the grid of the other.  For example,

	vop resample #1 ongrid #0 model #2
	vop morph #0,2

I've intended for a long time to make morph do the trilinear interpolation automatically (as done by "vop resample") if the grids didn't align or have matching sizes but have not gotten to that.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/11504

  Tom

	
On Feb 28, 2013, at 12:41 PM, Henning Stahlberg wrote:

> 
> Hi,
> 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?
> 
> Thanks,
> Henning.
> 
> 
> 
> 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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> 
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