[Chimera-users] Inifinite lattice minimisation

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 2 12:29:50 PDT 2012

Hi Kyle,
It only uses the atoms that are present (does not assume period boundary conditions).  I would not recommend using Chimera minimization on a very large system -- it does not use any distance cutoff and is thus quite slow.  Also the usual limitations of minimization: it will only go to a nearby local minimum, not the global minimum, so trapping in rather unfavorable conformations is a distinct possibility.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 2, 2012, at 12:23 PM, Kyle Morris wrote:

> Dear all,
> I am trying to do minimisations on a crystal system. I wonder if when chimera knows the unit cell will it minimise as an infinite lattice or do the copies need to be explicitly created before minimisation proceeds?
> Really appreciate any help/insight.
> Best wishes,
> Kyle

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