[Chimera-users] Adjusting the quality of surface while preserving other settings

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 4 10:06:52 PST 2011

Hi Sumitro,
Yes, you can adjust the surface "vertex density" without changing other settings.  I think the easiest way is to use the command "setattr" (set attribute), for example:

setattr s density 2.0


The default vertex density is 2, whereas the publication presets increase it to 10.  Besides "setattr", the value of this attribute can also be changed in the model attributes panel (in Model Panel, choose the surface model on the left and then "attributes" from the right) or the selection inspector (select surface, click green magnifying glass on bottom right corner of Chimera window, inspect "MSMS surface").  

Another setting that may have some effect on response, but I'm guessing not as much as the surface vertex density, is the subdivision quality.  It is analogous surface vertex density, but instead applies to ribbons, sticks, etc.  This is set in the Effects tool (under Tools... Viewing Controls)  or with the "set" command, for example:

set subdivision 2

Default is 1.5, publication presets increase it to 5.  However, I wouldn't bother with changing this unless response still seems slow after you decrease the surface vertex density.

Parameters affecting smoothness are discussed here...

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 3, 2011, at 10:30 PM, Sumitro Harjanto wrote:

> Hi Elaine,
> Is there a way to adjust the quality of the surface. I often use the preset publication setting to make the surface smoother before rendering images. But after activating publication quality, the speed will slow down, and I will experience lag (especially with large models) when I try to move/turn the models around. I wondering if I can toggle between ‘interactive’ and ‘publication’ quality for the surface only without affecting the background /ribbon settings..? thanks!   
> Cheers,
> Sumitro

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