[Chimera-users] Query about increasing resolution for vrml export

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 2 13:48:11 PST 2013


Hi Darren,
Tom described what to do for density map isosurfaces.

However, if you are instead talking about molecular surfaces, it is a separate parameter, "vertex density" … this can be changed in the Selection Inspector or with command "setattr," for example:

setattr s density 8

The default vertex density is 2.  This setattr command will only affect the molecular surfaces that already exist.  If you want to change the setting for subsequently calculated molecular surfaces, it can be done in the Preferences, category: New Surfaces; remember to click Save if you want your change to apply to future uses of Chimera.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces>

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 Dec 2, 2013, at 10:46 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Darren,
> 
>   There are two options in the Chimera Volume Viewer dialog in the Surface and Mesh Options panel (menu Features / Surface and Mesh Options), one called "Subdivide surface N times" and the other "Surface smoothing iterations 2, factor 0.3".  Turning the first one on will divide every surface triangle into 4 triangles.  And turning the second one on will move the surface vertices a little bit to give a smoother appearance.
> 
> 	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#surf-options
> 
> The finer surface will be export to VRML.  Also, be sure to make sure the "Step" size is set to 1 above the histogram in the volume viewer dialog since step > 1 subsamples the data and shows fewer triangles.
> 
>   A nicer smoother appearance would be achieved by interpolating the density map on a finer grid but Chimera does not have an easy way to do that.
> 
> 	Tom
> 
> On Nov 29, 2013, at 5:52 AM, Darren Gowers  wrote:
> 
>> Dear Chimera community,
>> 
>> Sorry to bother. I'm very interested in trying to increase the vrml export resolution (of any pdb model) so that more polygons are used to describe the curvature of the electron density more smoothly. There is a command in PyMol that does the equivalent (I think it is 'surface_quality'), but I'd rather use Chimera to generate vrml files!
>> 
>> Does anyone have any suggestions how to make molecular surfaces much smoother please?
>> 
>> Many thanks,
>> 
>> Darren
>> -- 
>> Dr Darren Gowers
>> Senior Lecturer in Biochemistry
>> School of Biological Sciences
>> University of Portsmouth
>> PO1 2DY
>> +44(0)2392 842057
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