Thanks Elaine, The preference value was set before calculating any surface. But, your explanation does make sense for a possible scenario for why the ASA would decrease with increasing the vdw radii. Thanks for your help, Ibrahim On 1/23/10 3:03 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:

Hi Ibrahim, First, make sure you set the New Surfaces preference value before showing the surface for the first time -- it would not affect a surface that already exists (even if it is hidden when you set the preference). If the surface already exists, you could change it to single-component by changing its attributes, such as with the command given in my previous message.

However, if the Reply Log says there is only one component of the surface in both sets of parameters, I think it is still possible for a surface area to decrease when the VDW radii increase. I'm imagining a case where there is a lot of concavity. Similar to the situation of an inside bubble shrinking or disappearing, a concave part of the surface could become shallower or much less extensive as the VDW radii are increased.

This is just a case I'm imagining. If you feel there is an error, please use "Help... Report a Bug" in the Chimera menu and be sure to describe exactly what you did to get the two area measurements, what two values you are comparing, and attach the PDB file of the structure (or just include the PDB ID in your description if it is taken directly from the Protein Databank). Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco