[Chimera-users] morph map and movie recording

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 26 10:36:28 PDT 2013


Hi Moumita,
Maybe the sequential fitting option of command "fitmap" will do what you want:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>

There is a video tutorial, 
<http://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/>

...but it might be slightly confusing because it shows non-sequential fitting first.  Only the second half of the video shows the sequential fitting command.  Also, it shows fitting multiple atomic structures into a larger map, but the command actually creates a map from each structure and then fits the maps into the larger map (i.e. you don't need the atomic structures).  However, you do have to put the smaller maps in approximately the right place before using the command.  Although "fitmap" also has a global search option, it cannot be combined in the same command with sequential fitting.

I hope this helps,
Elaine

On Apr 26, 2013, at 9:58 AM, Moumita Dutta wrote:

> 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.
> 
> Thanks,
> Moumita
> 
> 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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