How to measure the radius of density map
Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian -----Original Message----- From: chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request@cgl.ucsf.edu Sent: 2014年1月2日 15:00 To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 129, Issue 1 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. rate of a reaction (Haider Abbas) 2. Error in generating sqm for FAD (Isha) 3. Re: rate of a reaction (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jan 2014 10:51:05 +0530 From: Haider Abbas <haiderabbasphy@gmail.com> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] rate of a reaction Message-ID: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas
Hi Jian, Well, this idea is also partly manual: using Volume Tracer to place two markers (fake atoms) on the surface and then measuring the distance between them. (1) use Volume Tracer to place "markers" on the density map isosurface (Volume Tracer menu: Mouse... Place markers on surfaces, turn off other Mouse options). The manual part is where you click on the surface, and it might be tricky to put the markers where you want them. Maybe clip the surface so that it is cut across where you want to measure it, then try to put the markers on opposite sides of the rim. Volume Tracer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html> (2) measure distance between the two markers, just like for atoms, e.g. Ctrl-click one, Shift-Ctrl-doubleclick on the other, choose "show distance" from the resulting context menu. Happy New Year to you too, 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 Jan 3, 2014, at 11:08 AM, Jian Guan wrote:
Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian
Another approach is to use the Measure and Color Blobs. You can click on the virus surface and it will draw a box around it and report the exact dimensions of the box. The tricky part of this problem is deciding how you want to define "radius". Radius to a 5-fold vertex may be larger than radius along a 3-fold symmetry axis. And where do you define the surface of the virus, or do you measure to a maximum in density within the virus capsid along a radial line. I'm not sure what the commonly used definitions of virus radius are -- probably everyone does something different so the numbers are only meaningful to within maybe 5%. Tom On Jan 3, 2014, at 1:25 PM, Elaine Meng wrote:
Hi Jian, Well, this idea is also partly manual: using Volume Tracer to place two markers (fake atoms) on the surface and then measuring the distance between them.
(1) use Volume Tracer to place "markers" on the density map isosurface (Volume Tracer menu: Mouse... Place markers on surfaces, turn off other Mouse options). The manual part is where you click on the surface, and it might be tricky to put the markers where you want them. Maybe clip the surface so that it is cut across where you want to measure it, then try to put the markers on opposite sides of the rim.
Volume Tracer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
(2) measure distance between the two markers, just like for atoms, e.g. Ctrl-click one, Shift-Ctrl-doubleclick on the other, choose "show distance" from the resulting context menu.
Happy New Year to you too, 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 Jan 3, 2014, at 11:08 AM, Jian Guan wrote:
Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian
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participants (3)
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Elaine Meng -
Jian Guan -
Tom Goddard