[Chimera-users] show surface fails
goddard at sonic.net
Tue Dec 2 11:09:25 PST 2014
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.
> 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
> Department of Cell Biology
> Emory University School of Medicine
> Atlanta, GA 30322
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