[Chimera-users] show surface fails

Tom Goddard goddard at sonic.net
Tue Dec 2 11:09:25 PST 2014


Hi Criss,

  The Chimera molecular surface calculation fails on most large molecules (over 10,000 atoms) and is about 10x more likely to fail on 64-bit Windows than on other Linux or Mac.  The 32-bit Windows Chimera also fails less often than the 64-bit Windows, although more than Linux and Mac — so you might try 32-bit Chimera.  There are two newer versions of Chimera (1.9 and 1.10) but the surface calculation code has not changed so those will not improve the surface calculation success rate.

	Tom


> On Dec 1, 2014, at 6:53 PM, Hartzell Jr., Criss wrote:
> 
> I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? 
> 
> Criss Hartzell
> Professor
> Department of Cell Biology
> Emory University School of Medicine
> Atlanta, GA 30322
> 
> 
> 
> 
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