[Chimera-users] Alternative to the model panel

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 7 12:25:45 PDT 2010

Hi Rocco,
I recommend trying the ViewDock interface.  Normally this is used for viewing hundreds of docking hits in the context of the receptor site, but it might work really well in your application too.  However, this approach requires reformatting your file of structures so that it looks like a DOCK output.  If it is already a multi-molecule Mol2 file, it might just work as a "DOCK 4" output, or with minimal tweaking.

You would first start ViewDock (under Tools... Surface/Binding Analysis) and then in the dialog that appears, specify the quasi-"Dock results" file.

In addition to the man page, there is a ViewDock tutorial that includes a sample Dock 4 file:

Both include a picture (the same one) of the ViewDock interface, if you just want to take a quick look before investing more time.
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 Jul 7, 2010, at 12:05 PM, Varela, Lawrence Rocco wrote:

> Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more).  I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets.  Is there an alternative to using the model panel?  Like for example writing to file all the info that displays in the model panel including most importantly the model ids?

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