max density value using a script
Hi, I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.) Thanks for your help, 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, Here is Python code that computes max/min of one map subtracted from another. It assumes the maps are the same size and aligned. If they are different sizes or not aligned it will need some different code to do interpolation of one of the maps. https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py <https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py> More Chimera Python script examples are at https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts <https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts> Tom
On Sep 6, 2018, at 2:34 AM, Tamas Hegedus wrote:
Hi,
I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.)
Thanks for your help, 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Tom, Thanks for the suggestion. However, I can not access these links and I can not find any way to get access those scripts. ??? Thanks, Tamas On 09/06/2018 10:45 PM, Tom Goddard wrote:
Hi Tamas,
Here is Python code that computes max/min of one map subtracted from another. It assumes the maps are the same size and aligned. If they are different sizes or not aligned it will need some different code to do interpolation of one of the maps.
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py
More Chimera Python script examples are at
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts
Tom
On Sep 6, 2018, at 2:34 AM, Tamas Hegedus wrote:
Hi,
I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.)
Thanks for your help, 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- 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
Hi Tamas, I think you can see the links using http instead of https: http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2018, at 8:48 PM, Tamas Hegedus <tamas@hegelab.org> wrote:
Dear Tom,
Thanks for the suggestion. However, I can not access these links and I can not find any way to get access those scripts.
???
Thanks, Tamas
On 09/06/2018 10:45 PM, Tom Goddard wrote:
Hi Tamas,
Here is Python code that computes max/min of one map subtracted from another. It assumes the maps are the same size and aligned. If they are different sizes or not aligned it will need some different code to do interpolation of one of the maps.
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py
More Chimera Python script examples are at
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts
Tom
On Sep 6, 2018, at 2:34 AM, Tamas Hegedus wrote:
Hi,
I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.)
Thanks for your help, Tamas
Thanks - it works with http. On 09/07/2018 06:20 PM, Elaine Meng wrote:
Hi Tamas, I think you can see the links using http instead of https:
http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py
http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2018, at 8:48 PM, Tamas Hegedus <tamas@hegelab.org> wrote:
Dear Tom,
Thanks for the suggestion. However, I can not access these links and I can not find any way to get access those scripts.
???
Thanks, Tamas
On 09/06/2018 10:45 PM, Tom Goddard wrote:
Hi Tamas,
Here is Python code that computes max/min of one map subtracted from another. It assumes the maps are the same size and aligned. If they are different sizes or not aligned it will need some different code to do interpolation of one of the maps.
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/mapdiff.py
More Chimera Python script examples are at
https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts
Tom
On Sep 6, 2018, at 2:34 AM, Tamas Hegedus wrote:
Hi,
I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.)
Thanks for your help, 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
participants (3)
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Elaine Meng -
Tamas Hegedus -
Tom Goddard