[Chimera-users] Can you morph a ligand

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 9 12:47:11 PDT 2009

Hi Walt,
Thanks for the compliments -- and (even without the compliments) nice  
to hear from you!

The morph trajectory will only include the atoms that are in both  
input conformations.  They would have to be recognized as "atoms in  
common" in order to be retained.  I was going to say that perhaps this  
could be done with tricky renaming if the numbers of atoms were the  
same, but on second thought, that may not work.  I haven't tried it.

However, you can certainly still display those unique parts from the  
input models along with the trajectory, they just won't morph.   
Morphing with "hide conformations" turns off the model display of the  
input structures.  You could turn them back on with the "modeldisplay"  
command or by checking the "Shown" boxes in the Model Panel.   You  
would probably want to ~ribbon, ~disp the other parts of those input  

Say your input structures were models 0 and 1 and the morph trajectory  
is model 2.  To show (for example) the ligand and ions from model 1  
you could use the commands:

modeldisp #1
~ribbon #1
~disp #1
disp #1 & ligand
disp #1 & ions

In MD Movie, the tool that shows the morph trajectory, you could  
script it so that these atoms would appear at a certain frame.

If you are displaying ribbons, another thing you may want to include  
in a per-frame script is re-evaluating the secondary structure at each  
frame with the "ksdssp" command.  For default settings the command  
would simply be "ksdssp" without arguments.

Other than using the MD Movie dialog, another option for playing back  
the trajectory is the "coordset" command.  This is not integrated with  
the scripting in the MD Movie dialog, however.  Basically the same  
things could be done, just in a different way, possibly with some  
combination of the "coordset" and "perframe" commands:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 9, 2009, at 11:50 AM, Walter Fast wrote:

> Hi!
> Chimera is great - thanks again!  I use it all the time for research  
> and
> teaching.  I have a quick question:
> We have two different product-bound structures, but when I morph  
> between the
> two we loose the active site metal ions and the active-site  
> ligands.  Is
> there a way to include these as well?
> Thanks,
> Walt

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