[Chimera-users] surfaces

Elaine Meng meng at cgl.ucsf.edu
Thu May 25 09:24:06 PDT 2017

Hi Paul,
Sorry, Chimera doesn’t have special handling (like wraparound display) for periodic boundary conditions.

The Molecular Dynamics Simulation tool does have a “Constraints Etc.” section.  All I know about it is in the documentation:

Other programs may be better suited for simulating your system (faster, more options for solids or interfaces), although I don’t have specific suggestions.

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 24, 2017, at 1:33 AM, P. Buscemi <busce004 at umn.edu> wrote:
> Elaine,
> A conceptual question. 
> I'm trying to work with surfaces - large flat surfaces that proteins and
> polymers might adsorb. Think fibrinogen on medical devices.
> Chimera does not seem to like large surfaces in box. IF a portion of the
> surface slips outside the box, it goes to the other ( abnormal side).
> Constraining a portion of the surface does not help. Constraining all of the
> surface has not been tried.   I'd like to use a box  to keep the solvent and
> protein local.  
> Any suggestions on how to handle this, or point me to a URL ?  Can I
> constrain only in two directions  perhaps ?  or use a box size 30,30,
> infinite ?
> Best
> Paul Buscemi, Ph.D.

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