Hello, I have 2 maps that I want to combine into a single one. I cropped each map by reducing the box size. I now want to save the map that is displayed. Impossible?! “Save” fails to keep the relative orientation of the display. I get 2 cropped maps that are no longer correctly oriented with respect to each other. "volume add” also fails to preserve the relative orientation. The volume resample sounds like it could be helpful, but I don’t understand how to get the grid values that match the displayed box. I’ve now tried multiple options for over 5 hours solid and am at my wits’ end. Any hints greatly appreciated. Isabelle
Hi Isabelle, The command "volume add" adds the densities of the two maps. So where the overlap you will get higher density. Even if you are showing a surface of each map such that the surfaces do not overlap, the map values extend outside those surfaces and can create the higher densities. You can instead use "volume maximum #1,2" which will take the maximum density at each grid point so it will handle overlaps better. Using volume maximum worked for me in older ChimeraX 1.1, for example open 1080 from emdb open 1080 from emdb move z 130 model #2 coord #2 volume maximum #1,2 But in the current ChimeraX 1.2.5 it didn't get the combined map bounds right, and instead the resulting map had the bounds of the first map. I have fixed that bug -- the fix will be in tonights daily build. Tom
On Aug 25, 2021, at 5:22 PM, Isabelle Phan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
"volume add” also fails to preserve the relative orientation.
I meant to write: "volume add" fails to preserve the map densities.
Sorry, I. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hello Tom, YES, volume maximum on ChimeraX 1.1 did it. Thank you so much for fixing the current version, much appreciated. Isabelle
On Aug 25, 2021, at 6:06 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Isabelle,
The command "volume add" adds the densities of the two maps. So where the overlap you will get higher density. Even if you are showing a surface of each map such that the surfaces do not overlap, the map values extend outside those surfaces and can create the higher densities.
You can instead use "volume maximum #1,2" which will take the maximum density at each grid point so it will handle overlaps better.
Using volume maximum worked for me in older ChimeraX 1.1, for example
open 1080 from emdb open 1080 from emdb move z 130 model #2 coord #2 volume maximum #1,2
But in the current ChimeraX 1.2.5 it didn't get the combined map bounds right, and instead the resulting map had the bounds of the first map. I have fixed that bug -- the fix will be in tonights daily build.
Tom
<combine.png>
On Aug 25, 2021, at 5:22 PM, Isabelle Phan via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
"volume add” also fails to preserve the relative orientation.
I meant to write: "volume add" fails to preserve the map densities.
Sorry, I. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Isabelle Phan -
Tom Goddard