Zone map around center of rotation?
Hi, Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”). When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead. Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this? In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX. Cheers Oli
Ok so the same workaround does work in ChimeraX (I didn’t read the docs carefully enough…) so as an alias to crop all maps in a 15 Å sphere around the center of rotation, this does the trick: "alias map_sphere_15 surface unzone ##~num_residues; sel; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15; close #10000"
On Sep 1, 2023, at 4:26 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”).
When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead.
Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this?
In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX.
Cheers Oli
Hi Oli, While its possible to at some option to surface zone to make this easier, I'm reluctant to add features unless many people are going to use them. Can you explain why you want this? If you are trying to emulate Coot which always shows the map masked to a sphere around the center of view then the ISOLDE ChimeraX extension does exactly that. Tom
On Sep 1, 2023, at 3:02 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Ok so the same workaround does work in ChimeraX (I didn’t read the docs carefully enough…) so as an alias to crop all maps in a 15 Å sphere around the center of rotation, this does the trick:
"alias map_sphere_15 surface unzone ##~num_residues; sel; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15; close #10000"
On Sep 1, 2023, at 4:26 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”).
When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead.
Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this?
In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX.
Cheers Oli
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
No worries, this alias does the trick. Yes, ISOLDE does the same thing, with lots of extra stuff, and it’s great - this is better when I am just inspecting, not actively modeling (and doesn’t change other display characteristics of the map/model). Cheers Oli
On Sep 1, 2023, at 6:21 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
While its possible to at some option to surface zone to make this easier, I'm reluctant to add features unless many people are going to use them. Can you explain why you want this? If you are trying to emulate Coot which always shows the map masked to a sphere around the center of view then the ISOLDE ChimeraX extension does exactly that.
Tom
On Sep 1, 2023, at 3:02 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Ok so the same workaround does work in ChimeraX (I didn’t read the docs carefully enough…) so as an alias to crop all maps in a 15 Å sphere around the center of rotation, this does the trick:
"alias map_sphere_15 surface unzone ##~num_residues; sel; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15; close #10000"
On Sep 1, 2023, at 4:26 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”).
When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead.
Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this?
In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX.
Cheers Oli
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
One trick using Clipper: you can always hide the model associated with the map(s), then load in a second copy of the model to set up the atomic display to your liking. On Sat, 2 Sep 2023 at 08:28, Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
No worries, this alias does the trick. Yes, ISOLDE does the same thing, with lots of extra stuff, and it’s great - this is better when I am just inspecting, not actively modeling (and doesn’t change other display characteristics of the map/model).
Cheers Oli
On Sep 1, 2023, at 6:21 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
While its possible to at some option to surface zone to make this easier, I'm reluctant to add features unless many people are going to use them. Can you explain why you want this? If you are trying to emulate Coot which always shows the map masked to a sphere around the center of view then the ISOLDE ChimeraX extension does exactly that.
Tom
On Sep 1, 2023, at 3:02 PM, Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Ok so the same workaround does work in ChimeraX (I didn’t read the docs carefully enough…) so as an alias to crop all maps in a 15 Å sphere around the center of rotation, this does the trick:
"alias map_sphere_15 surface unzone ##~num_residues; sel; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15; close #10000"
On Sep 1, 2023, at 4:26 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”).
When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead.
Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this?
In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX.
Cheers Oli
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Oliver Clarke -
Tom Goddard -
Tristan Croll