[Chimera-users] Multiscale model of RNAP : fibrous aspect

Tom Goddard goddard at cgl.ucsf.edu
Fri Feb 27 09:57:34 PST 2009

Hi Damien,

  At 4 Angstroms you will see alpha-helices and beta-strands as you see 
here.  But there is a special problem with the multiscale tool on PDB 
entry 1l9u.  The trouble is that 1l9u has only backbone atoms N, CA, C.  
The multiscale tool uses to surface contour levels, one for models that 
include only CA atoms and one for models that contain additional atoms, 
usually all side-chain atoms.  So 1l9u is using the contour level 
appropriate for models that include side-chain atoms.  You can change 
these contour levels.  In the Multiscale Models dialog on the line that 
says "Resurface - resolution 4" there is a check button that shows 
additional options.  Change the "Threshold atom density" parameter from 
0.02 to maybe 0.004 (closer to the CA-only level of 0.002) then press 
Resurface.  The contour level is in number of atoms per cubic Angstrom.

  I've attached an image of what it looks like with that setting.  (I 
used silhouette edges, a white background, and glossy lighting (Chimera 
1.4 daily builds only) for my image.)


Damien Larivière wrote:
> Dear Elaine,
> I used the Multiscale Model tool to create a low resolution surface of 
> the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got 
> with a resolution 4 : a fibrous structure. So, I wonder what such a 
> fibrous aspect means or whether it means the tool has some 
> difficulties to create the surface with this specific protein ?
> Thanks for your help
> Damien
> ------------------------------------------------------------------------
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