[Chimera-users] surfaces

[P. Buscemi]

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.