[Chimera-users] Trouble understanding intersurf results

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 22 10:08:18 PDT 2020

Hi Kenward,
Sorry for the difficulties.  Intersurf was an implementation based on a paper, and has turned out to be somewhat of a novelty item that doesn't get much use.  I suspect there are bugs, or quirks that I failed to explain in the documentation (likely not having understood it myself).  Its main distinguishing characteristic is that the "inter"surface is not the molecular surface of either set of atoms in the interface but derived from both sets of atoms.  I too am mystified by the behavior of the "prune" option in the command, as it seems that, at least in your example, all prune values (even 0) give the same thing.  I can make a bug report but we are mostly focused on ChimeraX these days.

Depending on what you want the students to get from the exercise, there may be better alternatives, such as simply selecting atoms or residues with buried area in the interface between the two sets of atoms.  You could color those residues or their molecular surfaces.  (e.g. as in the "open book" image tutorial)

Maybe the problem is that the default surface wraps around all the proteins together?  You can get separate ones by using "split" beforehand to make each chain a separate model (as in that tutorial above), or if you can keep the chains in the same model but use "surfcat" to wrap K and M separately from B, e.g. commands:

surfcat bee :.b
surfcat kandm :.k:.m
surf bee
surf kandm

Another command of possible interest is "measure buriedArea" which will assign buriedSESArea and buriedSASArea attribute values to the atoms.  Then one can select atoms by ranges of those values.

measure buriedArea :.b :.k:.m
start Render by Attribute 
 (...that shows a dialog with histogram of values)
select @/buriedSASArea>2.0
(... or use the Select tab of that dialog to do the selection... whatever cutoff you like, of course)

Then you can "surf sel" or "color magenta sel" or whatever you were planning to do with the selection of interface atoms.
Sorry about the lame answer re Intersurf.  If there are other questions about how to accomplish various steps of the project, please don't hesitate to ask.  Best regards,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 21, 2020, at 8:49 PM, Kenward Vaughan <kay_jay at kvaughan.family> wrote:
> On 4/21/20 8:40 PM, Kenward Vaughan wrote:
> ...
> > The command I use is
> > 
> > intersurf   :.b   :.k,.m   pair atom   prune 3   bias 0.5   select
> > true
> > 
> > followed by adjusting the transparency.  The result surprised me,
> > both before and after lighting up the atoms and bonds.  I've attached
> > a (hopefully small) jpg.
> > 
> ...
> By the way, I just realized with further experimentation that a prune distance of 3 gives NO result ("no interface found") using the graphical interface with chain B and either K or M.  Changing this to 10 in my command still gives the same weird results...
> Kenward
> -- 
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