[Chimera-users] Surface calculation failed problem

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 9 11:55:44 PDT 2013


Hello fellow musician-scientist! (I'm just an amateur, though)

Unfortunately avoiding such numerical failures in molecular surface calculation is trial-and-error, and it is not always possible to avoid them.  However, there are a few other things to try, and in the event you cannot show a molecular surface, there are alternative kinds of surfaces that can be generated and colored.  There is a fairly new manual page on these various workarounds and alternatives:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

The alternative surfaces can be colored by electrostatic potential (ESP).  If you already have an ESP map from some program like APBS or DelPhi, you can open the map and use Electrostatic Surface Coloring.  If you don't already have a map, you could either 
(a) use the "coulombic" command (not the GUI, which depends on there being a molecular surface) with the "atoms" option:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
or 
(b) use the PDB2PQR tool (in menu under Tools... Structure Editing) to assign charges and then on the new copy of the molecule from PDB2PQR, run APBS (in menu under Tools... Surface/Binding Analysis) ... these both use web services, and the result is a map which can then be used by Electrostatic Surface Coloring.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

To color an alternative (nonmolecular) surface by hydrophobicity, you would first need to color the underlying atoms by hydrophobicity and then use the Color Zone tool (in menu under Tools... Volume Data) to make the surface match the atoms. If you have multiscale surfaces, this would only color the copy that has associated full atomic information, but the "msc" command could be used to apply the same coloring to all the other copies.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msc.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 Aug 8, 2013, at 8:00 AM, Hunter Brown wrote:

> Hello, I know this has been a somewhat common problem. When trying to display the molecular surface on a protein (I want to color by hydrophobicity and surface charge) I get the error "Surface calculation failed, mscalc returned code 5." I have tried increasing the VDW radius by 0.5, and lowering probe radius, and turning off 'display disjoint surfaces.' So far I have not been able to display the surface. I have a colleague that has displayed the molecular surface for a viral capsid, so I would think that I should be able to do it for a protein.
> 
> Is there anything else I can do? It would be really nice to create some hydrophobicity and surface charge images.
> Thanks in advance!
> -Hunter
> 
> Hunter Brown
> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
> University of New Mexico




More information about the Chimera-users mailing list