Question about "color sample" command
Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion) The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read? Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right? Finally is there a way to show a key for the coloring in chimerax? Many thanks for any advice you can provide. Sean
Hi Sean, Sorry, ChimeraX does not yet have color key drawings. One possibility is to use Chimera to draw it and then composite the images, but we understand that’s a pain since you have to manually enter the levels and colors into the Chimera Color Key dialog to match the settings you used in ChimeraX. In my ChimeraX tests, it does work to transform the map relative to the surface being colored and obtain a different coloring with the “color sample” command. By “work” I mean that the coloring changed, as well as the reported min,mean,max. These reported values are not for the map voxels overall but the values interpolated to the surface that is being colored (which could be an isosurface of another map). Thus if you move the map relative to the surface or vice versa, the reported min,mean,max will change. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> If you just move everything together, the coloring won’t change since the map and the surface will still have the same spatial relationship relative to each other. If you DO move one relative to the other and coloring doesn’t change, it would be a bug, but before you report anything with menu: Help… Report a Bug, make sure you get a recent version of ChimeraX and try it there first in case this is a bug that was fixed in the past. However, my understanding is that if you calculate a local-resolution map, it should already be in the correct register with the original map, so you shouldn’t need to move one relative to the other anyway. If you moved one and then just need to bring the other one into sync with again, see command “view” with “sameAsModels” option. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position> But say there is some situation that does require you to move a map relative to another and recolor. In that case, note “matchmaker” is not for maps… it is only for superimposing atomic protein or nucleic acid structures. You’d have to use some other method to transform one map relative to another, e.g. “move” with “models” option specified, or “fitmap,” or selecting the map with Ctrl-click and then using the “translate selected models” mousemode. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2019, at 2:15 AM, Sean Connell <sean.connell@gmail.com> wrote:
Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion)
The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read?
Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right?
Finally is there a way to show a key for the coloring in chimerax?
Many thanks for any advice you can provide. Sean
One minor correction to the paragraph below: there is a “matchmaker” option “bring” that allows you to move other models (potentially maps) along with the atomic models that are being superimposed. Elaine
On Aug 18, 2019, at 9:28 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: […] But say there is some situation that does require you to move a map relative to another and recolor. In that case, note “matchmaker” is not for maps… it is only for superimposing atomic protein or nucleic acid structures. You’d have to use some other method to transform one map relative to another, e.g. “move” with “models” option specified, or “fitmap,” or selecting the map with Ctrl-click and then using the “translate selected models” mousemode.
Hi Sean, The "color sample" command is supposed to handle the situation where the map and or surface models have been moved in the scene. This is a bug. I fixed it today, in tonight's ChimeraX builds. Tom
On Aug 18, 2019, at 2:15 AM, Sean Connell <sean.connell@gmail.com> wrote:
Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion)
The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read?
Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right?
Finally is there a way to show a key for the coloring in chimerax?
Many thanks for any advice you can provide.
Sean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Sean Connell -
Tom Goddard