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

Prasanna Venkatesh prasannavenkatesh1 at gmail.com
Tue Apr 16 14:54:04 PDT 2013

Thank you for your help Elaine and Rebecca :)

On Wed, Apr 17, 2013 at 6:48 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Prasanna,
> Please see the replies to the previous time you asked this question:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-March/008610.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-March/008612.html>
> 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
> ----------
> 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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