Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
Dear Dmitry, See command “measure correlation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat...> … or if you are fitting the maps (Fit in Map tool or “fitmap” command) it will be reported automatically in the tool dialog and/or Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> ..or you can click the “Update” button in the Fit in Map tool to get the value without fitting (moving) the map. I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 7:34 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
can you give me some details on this manner? I didn't figure out what I am gonna do exactly.thanks On Tue, Jul 9, 2019 at 8:50 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Dmitry, See command “measure correlation” < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat...
… or if you are fitting the maps (Fit in Map tool or “fitmap” command) it will be reported automatically in the tool dialog and/or Reply Log. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
..or you can click the “Update” button in the Fit in Map tool to get the value without fitting (moving) the map.
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 7:34 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Nail, There isn’t much else to say. your maps are open as #1 and #2, command: measure correlation #1 #2 … and then look in the Reply Log (menu: Favorites… Reply Log). Or to use a dialog, choose menu: Tools… Volume Data… Fit in Map, choose the two maps from the two pulldown menus in that dialog, and then click Update. The order is important (#1 #2 vs. #2 #1) and the contour level of the first map is important because by default the calculation will only use the grid points in the first map with values above its display contour level. See the manual pages in the links I sent previously for options such as using all values even if they are outside the contour surface. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 2:52 AM, Nail Besli <beslinail@gmail.com> wrote:
can you give me some details on this manner? I didn't figure out what I am gonna do exactly.thanks
On Tue, Jul 9, 2019 at 8:50 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Dmitry, See command “measure correlation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat...>
… or if you are fitting the maps (Fit in Map tool or “fitmap” command) it will be reported automatically in the tool dialog and/or Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
..or you can click the “Update” button in the Fit in Map tool to get the value without fitting (moving) the map.
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 7:34 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
measure correlation #0 #1? is it same measure correlation #1 #2? I mean two proteins structures to match. Is that right? On Tue, Jul 9, 2019 at 9:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nail, There isn’t much else to say. your maps are open as #1 and #2, command:
measure correlation #1 #2
… and then look in the Reply Log (menu: Favorites… Reply Log). Or to use a dialog, choose menu: Tools… Volume Data… Fit in Map, choose the two maps from the two pulldown menus in that dialog, and then click Update.
The order is important (#1 #2 vs. #2 #1) and the contour level of the first map is important because by default the calculation will only use the grid points in the first map with values above its display contour level. See the manual pages in the links I sent previously for options such as using all values even if they are outside the contour surface.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 2:52 AM, Nail Besli <beslinail@gmail.com> wrote:
can you give me some details on this manner? I didn't figure out what I am gonna do exactly.thanks
On Tue, Jul 9, 2019 at 8:50 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Dmitry, See command “measure correlation” < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat...
… or if you are fitting the maps (Fit in Map tool or “fitmap” command) it will be reported automatically in the tool dialog and/or Reply Log. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
..or you can click the “Update” button in the Fit in Map tool to get the value without fitting (moving) the map.
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 7:34 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
Hi Nail, Your previous message was a response to a question about map-map correlation. If you weren’t asking about that, you shouldn’t respond on the thread about volume comparison (see the subject line!) I answered your other question about matchmaker protein-protein superposition in a separate e-mail thread. Elaine
On Jul 9, 2019, at 3:32 AM, Nail Besli <beslinail@gmail.com> wrote:
measure correlation #0 #1? is it same measure correlation #1 #2? I mean two proteins structures to match. Is that right?
On Tue, Jul 9, 2019 at 9:17 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Nail, There isn’t much else to say. your maps are open as #1 and #2, command:
measure correlation #1 #2
… and then look in the Reply Log (menu: Favorites… Reply Log). Or to use a dialog, choose menu: Tools… Volume Data… Fit in Map, choose the two maps from the two pulldown menus in that dialog, and then click Update.
The order is important (#1 #2 vs. #2 #1) and the contour level of the first map is important because by default the calculation will only use the grid points in the first map with values above its display contour level. See the manual pages in the links I sent previously for options such as using all values even if they are outside the contour surface.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 2:52 AM, Nail Besli <beslinail@gmail.com> wrote:
can you give me some details on this manner? I didn't figure out what I am gonna do exactly.thanks
On Tue, Jul 9, 2019 at 8:50 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Dmitry, See command “measure correlation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat...>
… or if you are fitting the maps (Fit in Map tool or “fitmap” command) it will be reported automatically in the tool dialog and/or Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
..or you can click the “Update” button in the Fit in Map tool to get the value without fitting (moving) the map.
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2019, at 7:34 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Dmitry A. Semchonok -
Elaine Meng -
Nail Besli