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
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
Hi Elaine, Thanks for your quick response and the information. Brilliant support for this application, thanks. Best wishes, Kyle On 2 Aug 2012, at 20:29, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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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Elaine Meng -
Kyle Morris