calculate density from an AA model
Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model? Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/n... Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org
Hi Tamas, See command “molmap” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> Also, fitting atoms to a density map (Fit in Map GUI or “fitmap” command) has an option to simulate a map from the atoms and do map-map fitting. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2018, at 2:48 AM, Tamas Hegedus <tamas@hegelab.org> wrote:
Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model?
Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/n...
Thanks, Tamas
Dear Elaine, Thanks, it helped! On 09/06/2018 06:47 PM, Elaine Meng wrote:
Hi Tamas, See command “molmap” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
Also, fitting atoms to a density map (Fit in Map GUI or “fitmap” command) has an option to simulate a map from the atoms and do map-map fitting. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2018, at 2:48 AM, Tamas Hegedus <tamas@hegelab.org> wrote:
Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model?
Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/n...
Thanks, Tamas
-- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org
participants (2)
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Elaine Meng -
Tamas Hegedus