[Chimera-users] Failed surface calculation

Ibrahim Moustafa I.moustafa at psu.edu
Mon Jan 25 07:37:45 PST 2010

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,

On 1/23/10 3:03 PM, "Elaine Meng" <meng at 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

More information about the Chimera-users mailing list