[Chimera-users] Morphing

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 20 13:35:09 PST 2014

Hi Jim,
One more thing...
I didn't understand your mention of clustering.  Clustering doesn't really make sense for a morph trajectory; it is mainly for grouping similar conformations in an NMR ensemble or similar frames from molecular dynamics simulations.  It doesn't calculate or use residue interactions, it just compares the trajectory frames with one another.

On Jan 20, 2014, at 1:25 PM, Elaine Meng wrote:

> Hi Jim,
> If using the Find Clashes/Contacts dialog, you have to first "select" the atoms and then click the "Designate" button to designate them.  If you click the Help button on the dialog, it will show you its manual page, or you can see the same page on our website here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
> There are lots of ways to select atoms, for example command "select protein" if you want to select all protein atoms:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> This tutorial has a step-by-step example of using Find Clashes/Contacts:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> However, two things come to mind based on your description:
> (1) Find Clashes won't tell you what is changing across your morph per se; instead it will just find the clashes at each point (at each frame of the morph trajectory).  Not sure if that is what you wanted.  If you just want to see where the CA atoms deviate from each other when the structures are superimposed, you could superimpose them with MatchMaker with the option to show the sequence alignment turned on, and then in the resulting sequence alignment menu, choose Headers... RMSD.
> (2) since you may want to calculate clashes for each point in your morph trajectory, it may be more convenient to use the command "findclash" instead of the GUI.  Then the atoms would be specified in the command instead of as a selection. The MD Movie dialog that is showing your morph allows defining a per-frame script, that is, one or more commands to be run at each frame of the trajectory.  See "per-frame scripts" in the MD Movie manual page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> This tutorial has an example of defining a per-frame script.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
> I don't know if structureViz is available for Cytoscape 3.  At least for Cytoscape 2.x, one would use the Plugins menu to get various plugins including structureViz.
> 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 Jan 20, 2014, at 5:17 AM, James Naismith wrote:
>> I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work.
>> I am using a MAC OSX latest version.
>> I have created my morph which is running nicely.
>> What I would like to do is analyse the morph for VDW clashes.
>> (That is in going from structure 1 to structure 2, what residues would have to move).
>> First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations
>> When I click OK or apply I get a new box residue interaction contact parameters
>> This always generates an error “No atoms designated for clash detection’
>> I seem only to have four options 
>> themselves
>> all others atoms (default)
>> other atoms in same model 
>> second set of designated atoms
>> Any help gratefully received
>> (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version)
>> best
>> Jim
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