[Chimera-users] surface display

[Eric Pettersen]

A few additional comments:

1) We _are_ working on a replacement library.  Really.  It's just has  
proven very tricky to get the geometry right in all cases.

2) Aside from changing the VDW radii, adding hydrogens to your  
structure (or deleting them if you have them already) may also do the  
trick.  Tools->Structure Editing->AddH.  That's also in the post that  
Tom references but he only mentioned the vdwdefine method.

3) In recent versions of Chimera, the vdwdefine syntax would be  
"vdwdefine +0.01" rather than "vdwdefine * * +0.01"

4) Once surfacing fails in an instance of Chimera, it won't work again  
no matter what you try.  You have to quit and restart in order to try  
the "tricks".

--Eric

On Mar 9, 2007, at 12:39 PM, Tom Goddard wrote:

> Hi Markus,
>
>   This is a problem with the surface calculation library MSMS used by
> Chimera.  It crashes on specific PDB files.  It is described more in
> this post:
>
>
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-February/ 
> 000685.html
>
> which suggest you use Chimera command
>
>     vdwdefine * * +0.01
>
> to make the atom radii 1/100 Angstrom bigger which may circumvent the
> crash. Trying to surfce fewer residues generally does not fix the
> problem because Chimera still computes the whole surface and then just
> limits the display to the few residues you selected.
>
>   Here is the Chimera bug report about this problem.
>
>
> http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl? 
> cmd=view&pr=1295&database=chimera
>
>   Tom
>
> Markus Voehler wrote:
>> Tom
>>
>> I have installed the new version and the same thing happens. Here is
>> what I do:
>> 1) open pdb (3003 atoms)
>> 2) display round ribbon, hide atoms/bonds
>> 3) action --> surface --> show also tried it on a smaller selection of
>> a few residues.
>>
>> I have submitted the chimera error report and have attached the crash
>> report. Any ideas would be appreciated.
>>
>> Markus
>>
>>
>> On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote:
>>
>>> Hi Markus,
>>>
>>>  Is your problem with molecular surfaces (menu Actions / Surface /
>>> show) or contour surfaces of volume data?
>>>
>>>  In either case you should first try a newer version of Chimera.  I
>>> recommend trying the snapshot 1.2352 released this week (scroll down
>>> the Chimera download page a little).
>>>
>>>  http://www.cgl.ucsf.edu/chimera/download.html
>>>
>>>    Tom
>>>
>>
>
>
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