[Chimera-users] Tube representation of the motion projections along the eigen vectors

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 16 14:48:30 PDT 2013

Dear Prasanna,
Please see the replies to the previous time you asked this question:


I assume you meant showing results from Gromacs in Chimera.   If you really meant showing them in Gromacs, then you should ask the Gromacs mailing list.

I don't know any more than in my previous answer, as I have never done this myself.   In Rebecca's answer, she said you would first have to generate multiple PDB files showing the different conformations along the motion eigenvectors.  You cannot use Chimera for that, you need to find some other way.  She suggested using R.  Then, as she said, you could open the PDB files in Chimera and show them as licorice (Actions... Ribbons... licorice) and/or use Morph Conformations (under Tools... Structure Comparison) if you want to show the eigenvector motions dynamically. Click the Help button on that tool for instructions on how to use it.

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 16, 2013, at 2:26 PM, Prasanna Venkatesh wrote:

> Dear all,
>    I request you to give me the steps for "Tube representation of the motion projections along the eigen vectors" in Gromacs. Please give me step wise details with the input file types required. Thank you in advance.
> Prasanna.

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