[Chimera-users] "Surface calculation failed, mscalc returned code 5"

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 6 15:21:46 PST 2010

Whoops, sent the wrong "previous post" link.  Here is the one I meant to send.


On Dec 6, 2010, at 3:16 PM, Elaine Meng wrote:

> Hi Sumitro,
> This is a commonly reported problem and represents a numerical failure of the MSMS code included with Chimera for calculating molecular surfaces.
> Sometimes when there is an error, it can still fall back to a "single component" calculation.  The problem may be in some inside bubble, whereas the "single component" is the main outer surface.  If you get that "falling back" message but it still shows the surface you want, you can ignore the message.
> If you didn't get any surface, however, there are several things to try; unfortunately none is a magic bullet that works in all situations.   One easy thing to try if your structure has multiple chains is to simply split the model before showing the surface (just enter the command "split"), which makes each chain have its own separate surface.   If that doesn't work, or you didn't want separate surfaces, see this previous post for additional things to try:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002954.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 Dec 6, 2010, at 1:35 AM, Sumitro Harjanto wrote:
>> Hi Meng,
>> I’ve run into this problem a few times when I wanted to calculate and show the surface of a pdb model.
>> I got the following on my reply log:
>> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1
>> Calculation of some surface components failed.
>> Falling back to single-component calculation.
>> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0
>> Surface calculation failed, mscalc returned code 5
>> Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn’t work. Any suggestions?
>> One particular file that gives me the problem is 1IGT from PDB. I’ve tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D.  but still the problem persists.
>> Thanks!
>> Cheers,
>> Sumitro

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