[Chimera-users] Can you morph a ligand

Walter Fast waltfast at mail.utexas.edu
Wed Sep 9 13:06:34 PDT 2009

Thanks Elaine, we'll give it a try.

For teaching, this Friday I'll use Chimera in lecture with red/cyan glasses
for everyone - from my view it looks just like an old 50s 3D movie audience!

You are always so helpful - Thanks!



Walter Fast, Ph.D.
Associate Professor

The University of Texas at Austin
College of Pharmacy
The Division of Medicinal Chemistry
Phone:  (512) 232-4000
Fax:    (512) 232-2606
Lab:    (512) 471-5839
Email:  WaltFast at mail.utexas.edu

On 9/9/09 2:47 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
> 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
> structures.
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per
> -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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>
> 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 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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