Helical Parameter estimate using Chimera
Hi All, I want to estimate Helical parameter ( Helical Rise, Twist, asymmetric sub unit, per turn ) of Tau filament for Reference Module generation using Chimera. Is it possible to estimate from raw micrographs or 2D Class Average by Chimera? I was wondering if any of you can provide me procedure if any, will be a great help. Eagerly waiting for your reply. Thanks in Advance, Reja [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sign...> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sign...> 04/14/19, 8:11:49 PM
Hi Reja, There is a “measure symmetry” command but it is somewhat limited. "Check each specified volume data set (map) for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems. Helical symmetry can be considered if approximate parameters are supplied.” For command syntax and further details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 14, 2019, at 5:16 PM, Rejaul Hoq Nayem <nayem1chem@gmail.com> wrote:
Hi All, I want to estimate Helical parameter ( Helical Rise, Twist, asymmetric sub unit, per turn ) of Tau filament for Reference Module generation using Chimera. Is it possible to estimate from raw micrographs or 2D Class Average by Chimera? I was wondering if any of you can provide me procedure if any, will be a great help. Eagerly waiting for your reply. Thanks in Advance, Reja
It would only work on 3D volume data that isn’t too noisy since it relies on self-correlation upon rotation/translation. Elaine
On Apr 15, 2019, at 9:45 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Reja, There is a “measure symmetry” command but it is somewhat limited.
"Check each specified volume data set (map) for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems. Helical symmetry can be considered if approximate parameters are supplied.”
For command syntax and further details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 14, 2019, at 5:16 PM, Rejaul Hoq Nayem <nayem1chem@gmail.com> wrote:
Hi All, I want to estimate Helical parameter ( Helical Rise, Twist, asymmetric sub unit, per turn ) of Tau filament for Reference Module generation using Chimera. Is it possible to estimate from raw micrographs or 2D Class Average by Chimera? I was wondering if any of you can provide me procedure if any, will be a great help. Eagerly waiting for your reply. Thanks in Advance, Reja
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participants (2)
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Elaine Meng -
Rejaul Hoq Nayem