[Chimera-users] morph map and movie recording

Moumita Dutta dutta at bio.fsu.edu
Fri Apr 26 09:58:33 PDT 2013

Hi Elaine,

The sop hideDust option worked. Is there any way to use the fit in map  
option from the command line to fit other maps all at a time in one map.


  Quoting "Elaine Meng" <meng at cgl.ucsf.edu>:

> Hi Moumita,
> Our expert in this topic is not here (will be back next week), but  
> in the meantime I will try to guess what is happening and give some  
> hints.
> The "vop morph" command creates a new map, by default assigning it  
> the lowest unused model number.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>
> I'm guessing the problem is that you set threshold and used hide  
> dust for the input maps before using "vop morph", but unfortunately  
> those settings do not apply to the new map.
> WIth the Morph  Map graphical interface, you can first create the  
> morph map, then use Hide Dust to hide the dust in the new map and  
> Volume Viewer to adjust its threshold (or corresponding commands  
> "sop hideDust" and "volume" with the "level" option), and then go  
> back to the Morph Map Interface and "Play" and/or "Record" that  
> existing map without re-creating it.  However, the "vop morph"  
> command is all-in-one and creates the map right before playing it,  
> so there is no opportunity to change the new map's settings and hide  
> its dust in between.  Unfortunately I don't know how to solve that  
> problem.  In other words, I don't know how to separate creation of  
> the morph map and playback of the morph in a command script, so that  
> you could control its threshold and dust display with other commands  
> in between.  I'm hoping our expert will be able to suggest something  
> when he returns.
> The part about the input maps displaying and orientations changing  
> makes no sense to me, other than you may be using their model  
> numbers (or no model numbers) instead of just the model number of  
> the new map in subsequent commands in the script.  By default the  
> "vop morph" command should hide the input maps (hideOriginalMaps  
> true).
> Best,
> 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 Apr 25, 2013, at 4:07 PM, "Moumita Dutta" <dutta at bio.fsu.edu> wrote:
>> Hello,
>> I am trying to morph more than two maps at a time so I am using vop  
>> morph instead of Morph map. I am following the mini-video animation  
>> example script of vop morph using the recommended chimera 1.7  
>> version 2013. The script actually recorded the movie but in the  
>> movie threshold changed from what I set and it turned some maps to  
>> x 90 degree not all and it is not showing the morph animation only  
>> the superimposed maps. Another problem is though I remove the dust  
>> after loading the maps but it came back in the morph and in the  
>> movie as well.
>> How can I fix the problems and generate the movie ?
>> Moumita

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