[Chimera-users] surface failures

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 11 10:22:06 PDT 2014


Hi Julian,
That image is too small to read, but I'm sure it is the same type of error we were discussing earlier. 

I guess you didn't try #3 in "surface calculation failures and workarounds" because the "molmap" method always works.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

For example, I opened 3u5e and 3u5d.  I could see chain 1 included some RNA + a bunch of osmium hexammine (OHX) residues.  I thought you probably didn't want the OHX included in the surface, so the molmap command could be something like this

molmap  :.1&~:ohx  5

… where the specifier means chain 1 AND NOT residue OHX.  See result in attached image. To use all of chain 1 (but again, I don't think that is what you want) it would just be

molmap  :.1  5

The 5 is the resolution of the surface, but you might want to try other values.  There are also other parameters like gridspacing that will affect the appearance of the surface.  See the molmap man page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

Best,
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 Mar 11, 2014, at 8:25 AM, Julian Marzi <julian.marzi at googlemail.com> wrote:

> Dear Elaine Meng,
> I tryed the surface option in different pdb files (also the 50S of E.coli) and always the same error (code 11- see attached). I also tried the different option of the webpage (Surface calculation failures and workaround).
> I would like to have the surface structure of the chain 1 (25S of the yeast ribosome). Now I use the pdb file 3U5E and 3U5D. Please can you help me. Chimera is such a beautiful program and it always looks good, but in the most publication the surface structure is built up. 
> Thank you
> Best regards
> Julian 
> 
> <PastedGraphic-1.png>
> Am 06.03.2014 um 19:20 schrieb Elaine Meng <meng at cgl.ucsf.edu>:
> 
>> Dear Julian,
>> The surface failure is a numerical thing that may differ on different machines, and there is not a consistent recipe for how to solve the problem.  Please see this page on possible solutions, including showing some alternative types of surface instead of a "molecular" surface:
>> 
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
>> 
>> 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 Mar 4, 2014, at 3:31 AM, Julian Marzi <julian.marzi at googlemail.com> wrote:
>> 
>>> Dear Chimera,
>>> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it doesn't work. Mscalc returned code 11 is shown. If I split the 60S every chain show the surface except the first strain (25S). How can I show the surface from the first chain?
>>> Thank you very much
>>> Best regards
>>> Julian Marzi

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