[Chimera-users] Chimera Surface Calculation

Tom Goddard goddard at sonic.net
Tue Jul 17 10:34:54 PDT 2012

Hi Robert,

   Unfortunately the MSMS molecular surface calculation code has bugs 
and so it fails to compute surfaces for most large (>10,000 atom) PDB 
models.  The surface calculation has essentially no chance of working 
with a model of 110,000 atoms such as your half-virus.  That said I used 
the 64-bit Mac Chimera and split the model by chains and it surfaced 
fine -- see attached image.  The Windows Chimera versions have the most 
surface calculation failures especially 64-bit Windows Chimera, and Mac 
and Linux are substantially better.

   So I made the image bmv.jpg with "split #0; surf; rainbow model".  
After the split, it is odd that many of the subunits have no atoms 
shown.  I used Actions / Atoms / Show to show them.

   If you don't require a solvent excluded surface (rolling a ball over 
the atoms to get the surface), you can use a Gaussian surface.  The 
second image bmv5.jpg was made without splitting the model using a 5 
Angstrom density map.

     molmap #0 5 model #1
     volume #1 step 1
     color lightblue :.A
     color lightyellow :.B
     color pink :.C
     color red :.D-K
     scolor #1 zone #0 range 10


> Hi Tom,
> I am a post doc at Indiana University in the Biochemistry department, and I was at the chimera tutorial  you gave to our department through David Morgan.  I wasn't sure who to write with this question, so I thought I would start with you but if this is more appropriate for someone else, just let me know.
> Forever ago I used Viper to create a 60 subunit (or 1/2) capsid for BMV, and made several models for publications.  That .pdb file that I made no longer works within Chimera, and I have literally tried everything to get it to work.  Additionally, it seems Viper no longer lets you make those .pdb files anymore.  I have tried changing the atomic radii probe radius, the vertex density, set the disjoint surfaces to false, and every combination of those things.  Additionally, when I use the split command, it either only shows a weird surface or no surface at all, and almost completely obliterates the original structure.  If you know another way to do this, I would really appreciate any advice here as I have spent hours reading through forums.  I attached the .pdb to this email.  Again I really appreciate your help.
> Thanks in advance,
> Robert

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