[Chimera-users] Surface calculations difficulties

[Tom Goddard]

Hi Sarah,

  It is frustrating that the Chimera solvent excluded surface code is not reliable.  We replaced that code in our next generation ChimeraX program which is not yet released.  But the new surface calculation is also in Chimera if you use a secret grid option, command

	surface #3 grid 0.5

The value is the grid spacing, 0.5 Angstroms works well.  This calculation will always work, but we don’t advertise this because the resulting surface does not know which atoms are associated with which surface patches.  (We just put it in Chimera for some basic testing.)  But you can use this surface for electrostatic coloring.

	Tom

> On Nov 9, 2016, at 3:50 PM, Sarah Piper <s.piper at imb.uq.edu.au> wrote:
> 
> Hi everyone,
> 
> I’ve been struggling with getting the structure surface of my molecule shown (actions  surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> ), I can’t get all needed surfaces displayed.
> 
> Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes.
> 
> A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? 
> Or do the .pdb files have to be in a certain format?
> 
> 
> I usually get the following errors:
> 
> "Surface calculation failed, mscalc returned code 2.
> 
> Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface.  If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at
> 
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>”
> 
> 
> My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation).
> 
> I'd appreciate any feedback or reply!
> 
> 
> Many thanks for your help,
> 
> 
> Sarah
> 
> 
> 
> 
> …………………………………………………………………..
> Sarah Piper, PhD student
> University of Queensland, St Lucia, 4072 QLD, Australia
> 
> Phone: +61 7 3346 2325
> Email: sarah.piper at uq.edu.au <mailto:sarah.piper at uq.edu.au>
> 
> 
> 
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