[Chimera-users] morph problem

Andres Palencia palencia at embl.fr
Wed Mar 2 09:57:54 PST 2011

  Dear Chimera Users,

I am trying to morph the complex1 and complex2 from the same system 
(protein-RNA) to make a video monitoring the conformational changes.
As complex 1 is missing one domain and a helix (not visible in the 
crystal structure), I need to remove these parts in complex 2 to have an 
equal number of atoms in both complex and could morph it.
The resulting video is not so nice because shows the gaps corresponding 
to the missing part. So, to avoid that, I have modelled the missing part 
in the complex 1 to have the same atoms, and afer morph it again to make 
the video, but this is not working.
In the transition between complex 1 and complex 2, the RNA encounter one 
helix on the way that needs to move out to let the RNA  to get the 
position observed in complex 2. If I take out this helix, the video can 
perfectly be done, but still is not perfect because show gaps.

Anybody could give an idea in how to solve the problem? We need the 
video to include in a publication,.

Thanks in advance,

Andrés Palencia

Andres Palencia, PhD
Protein RNA Group
EMBL Grenoble Outstation
6 rue Jules Horowitz
BP181, 38042 Grenoble Cedex 9, France
email: palencia at embl.fr
phone:  + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab)
fax:    + 33 (0)476 20 7199

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