[Chimera-users] Chimera 1.2176: surfaces fail for some structures?

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 13 12:01:17 PST 2006

Hi Anna,
	That bug has actually been around since time immemorial -- we  
finally remembered to add it to the release notes.  It is a behavior  
of the underlying MSMS library for certain particular geometries.  We  
are working on a replacement library but it isn't ready yet.  So  
there really isn't any version you can change to that won't have the  
	There are some workarounds.  Because the problem depends on the  
exact geometry of the structure, changing that geometry only slightly  
will frequently allow surfacing to start working.  So for example if  
your structure lack hydrogens, adding hydrogens (the AddH tool) will  
often allow the surface to work.  Keep in mind that once surfacing  
fails, it won't work again in that same instance of Chimera -- you  
will have to quit and start Chimera again to try the workaround.   
Another way to slightly change the geometry is to modify the VDW  
radii slightly.  Using the command line (Favorites->Command Line),  
the command "vdwdefine * * +0.01" will increase all vdw radii by 0.01  
angstroms -- you could try other values also.
	Sorry we don't have a good solution yet.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Feb 13, 2006, at 7:35 AM, Anna Feldman-Salit wrote:

> Hello,
> I have noticed that for 1.2199 version there is a "know bug" of  
> surface
> failure.
> We have been working with 1.2176 version (which is probably even not
> release version). Apparently, I have the same problem with some of
> molecules (working with 1.2176). Is it occasionally or there is a  
> "known
> bug" for 1.2176 too?
> Can you maybe recommend some version that has not such a problem?
> Thank you in advance!
> Sincerely,
> Anna.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20060213/cba8de8c/attachment.html>

More information about the Chimera-users mailing list