[Chimera-users] Inifinite lattice minimisation

Kyle Morris Kyle.Morris at sussex.ac.uk
Fri Aug 3 01:01:20 PDT 2012

Hi Elaine,

Thanks for your quick response and the information. Brilliant support for this application, thanks.

Best wishes,

On 2 Aug 2012, at 20:29, Elaine Meng <meng at cgl.ucsf.edu>

> 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
> ----------
> 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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