[Chimera-users] about volume viewer

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 21 09:38:24 PDT 2015


Hi Lei Zhang,
It is not totally automatic, but after you have calculated the expected volume, you can keep adjusting the level and measuring the resulting volume until you get something close, as described here:
<http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2>

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 Apr 20, 2015, at 6:43 PM, 张雷 <leizhang at hsc.pku.edu.cn> wrote:

> Hi, the experts of Chimera,
> I am a new user of Chimera and have a question to consult you. When I display a 3D model in the volume viewer, I found that there was an original value of the level, as the attached figure shown. If I increased and decreased the values of level, the densities of 3D models were different. Therefore, how to deternime the right value of level for a protein. It is known that the average density of proteins is 1.35 g/cm3; If a protein has a molecular weight of 1350 kDa, and 1 Da = 1.66054E-27 kg; therefore, the protein volume is 1661 nm3.If I want to display the volume of 1661 nm3 in chimera, how can I decide the value of level? In another words, how can I calculate the value of level from the actual volume of a protein? Thank you!
> Best wishes!
> Lei Zhang
> Peking University, Beijing, China




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