[Chimera-users] about volume viewer

张雷 leizhang at hsc.pku.edu.cn
Tue Apr 21 20:52:41 PDT 2015


Hi Elaine,

It works very well. That's great! Thank you!

Best wishes,


Lei Zhang




> -----原始邮件-----
> 发件人: "Elaine Meng" <meng at cgl.ucsf.edu>
> 发送时间: 2015-04-22 00:38:24 (星期三)
> 收件人: "张雷" <leizhang at hsc.pku.edu.cn>
> 抄送: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> 主题: Re: [Chimera-users] about volume viewer
> 
> 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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