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
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...> 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@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
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. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/volume.html Tom
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...>
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@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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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@cgl.ucsf.edu> 发送时间: 2015-04-22 00:38:24 (星期三) 收件人: "张雷" <leizhang@hsc.pku.edu.cn> 抄送: "chimera-users@cgl.ucsf.edu" <chimera-users@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...>
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@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
participants (3)
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Elaine Meng -
Tom Goddard -
张雷