[Chimera-users] Manipulate individual hexagons/pentagons in cage builder

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 10 08:36:55 PST 2015

Hi Vamsee,
Seems like an under-determined or under-defined problem, as one might expect an infinite number of ways to misassemble a set of subunits.

If there were any experimental information on the nature of the misassembly, that might help, but even so, I don't have elegant ideas of how to generate it in Chimera.  The cage is a created as a bunch of markers (fake atoms, where each is a separate residue) with links (fake bonds) between them. If you can select just the markers in an individual polygon with the mouse, then you can move them manually (leaving the others unmoved) with the Movement Mouse Mode tool. It's in the menu under Tools… Movement, and you would use the mode to "Move selection".  Doing this several times might be tedious, and the resulting model might be a figment of your imagination, however!

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 Feb 9, 2015, at 3:25 PM, vamsee <vamseedharr at gmail.com> wrote:

> Hello Elaine,
> I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. 
> Thank you yet again,
> Vamsee

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