[Chimera-users] Display atoms after multiscale model

vamsee vamseedharr at gmail.com
Mon Dec 1 10:45:15 PST 2014

Hi Elaine,

I have been trying to calculate SASA of some multimeric proteins and in
certain cases negative values come up. Is there an explanation to this? Is
it actually telling me something about the surface area and is there
workaround to getting the actual values?

Thank you


On Wed, Oct 29, 2014 at 8:01 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Vamsee,
> Now there is a “measure buriedArea” command, so it should be much
> simpler.  However, you have to make sure that atoms are loaded for the
> subunits of interest, not just the low-resolution multiscale surfaces, and
> be very careful to specify only the intended atoms in the command (for
> example, you might want to delete any water, ligands, etc. first to make it
> easier).  Even though the displayed molecular surface would automatically
> exclude stuff like water, the buried area calculation does not.
> <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
> The Multiscale low-resolution surfaces are calculated differently and
> would have a different surface area than the standard molecular surfaces
> (measure buriedArea calculates the standard ones).  Seems logical that the
> results with low resolution surfaces would be less accurate.  See the
> Multiscale documentation, especially the sections “low-res surfaces” and
> “loading atomic coordinates”:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html
> >
> I hope this helps,
> 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 Oct 29, 2014, at 2:15 PM, vamsee <vamseedharr at gmail.com> wrote:
> > Hello,
> > I am working on a virus capsid and trying to figure out the buried
> surface area between subunits (similar to what ViperDB has. I have to do
> this for a few capsids and I am trying to automate this to the maximum
> possible extent. I have been able to follow the steps in this link Buried
> surface area calculation and manually calculate the information. Are there
> commands available to do the same?
> > Also, what is the difference between the surfaces created using a
> multiscale model and surfaces computed from the atom-spec? Would this
> difference in the surface affect the calculation of the buried surface
> area? And if it does affect it which one be a more accurate representation?
> > Thank you
> > Vamsee
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