[Chimera-users] about volume viewer

Tom Goddard goddard at sonic.net
Tue Apr 21 10:01:53 PDT 2015

Hi Lei,

  The Chimera volume command can set the level to obtain a specified enclosed volume

	volume #0 enclose 1661000

To show the command-line use menu Favorites / Command Line.  I used 1661000 for 1661 nm**3 because usually Angstroms are used for units instead of nanometers (because molecular PDB models use Angstroms).  The grid spacing of your map needs to be set correctly for this to work — it is given in the Volume Viewer dialog menu Features / Coordinates and is called “voxel size”.  That number should be given in Angstroms if you want to use Angstrom units.



> On Apr 21, 2015, at 9:38 AM, Elaine Meng  wrote:
> 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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