[Chimera-users] Failed surface calculation

Ibrahim Moustafa I.moustafa at psu.edu
Fri Jan 22 17:44:42 PST 2010

Thanks Elaine for the reply.

The trick of changing the vdw radius (vdwdef +0.05) worked; then I got the
default back by "~vdwdef".

 I'm not sure whether this affect the accuracy of the calculation. Because,
I noticed by increasing the vdw radius by "+0.05" the value of the volume
got increased from 111.0e3 to 113.6e3 (2.3%), which is expected. However,
the measured area decreased from 36.73e3 to 36.2e3, which does not make
sense to me (please correct me if I am missing something here).

 Do you have any comment?!


On 1/22/10 7:32 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Dear Ibrahim,
> This is common and represents a numerical failure of the MSMS code
> included with Chimera for calculating molecular surfaces.
> The first thing to do is make sure you have a fairly recent version
> of Chimera, say 1.4 from Dec 2009 or newer.  Although we have not
> eliminated the failures, we have made some improvements that reduce
> their frequency.
> 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 that's
> what happened, but it still looks like you got the surface you want,
> you can ignore the message.
> If you didn't get any surface, however, there are several things to
> try, as mentioned in several previous posts (links below).
> Unfortunately none is a magic bullet that works in all situations.
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003816.html>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/
> 003096.html>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/
> 002954.html>
> Because of the MSMS problems, we have been working for many months on
> code to replace it, but it is not yet available.
> 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 Jan 22, 2010, at 4:10 PM, Ibrahim Moustafa wrote:
>> Dear Chimera,
>>  I¹m trying to calculate the surface for a protein but I get an error
>> ²Surface calculation failed, mscalc returned code 5².
>> I tried to change the probe size from 1.4 to 1.5 or 1.7 but still
>> getting
>> the same error. I know there is some issue with
>> The code that calculates the surface (if I¹m not wrong) but I
>> wonder if
>> there is a way to get around this. For some smaller pdb files I
>> don¹t have
>> this problem.
>> I¹m not sure if the size of the protein is a factor here. The
>> protein having
>> the problem is a single chain protein with 880 amino acids.
>> Any advice?
>>   Thanks for help.
>>  Ibrahim

More information about the Chimera-users mailing list