Hi all,
I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera?
Best, -Alex Noble
Hi Alex, Sure! There is a “Values at Atom Positions” tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc.
The tool is in the menu under Tools… Volume Data. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html
Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
The coloring could also be done with the “rangecolor” command, and labeling with “labelopt” (or menu Actions… Label… other). With labelopt you can specify a format so that you don’t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name:
labelopt info %(value_name_of_map).3f
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2015, at 1:33 PM, Noble, Alex ajn10d@fsu.edu wrote:
Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble
Just to clarify, after the “labelopt” command you would still have to use “label” to actually display the labels!
Elaine
On Jan 30, 2015, at 2:36 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Alex, Sure! There is a “Values at Atom Positions” tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc.
The tool is in the menu under Tools… Volume Data. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html
Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
The coloring could also be done with the “rangecolor” command, and labeling with “labelopt” (or menu Actions… Label… other). With labelopt you can specify a format so that you don’t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name:
labelopt info %(value_name_of_map).3f
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2015, at 1:33 PM, Noble, Alex ajn10d@fsu.edu wrote:
Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Wonderful! Thank you Elaine and Tom, much appreciated=)
-Alex ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, January 30, 2015 5:49 PM To: Noble, Alex Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Using Chimera to measure voxel densities
Just to clarify, after the “labelopt” command you would still have to use “label” to actually display the labels!
Elaine
On Jan 30, 2015, at 2:36 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Alex, Sure! There is a “Values at Atom Positions” tool to get the values, interpolating as needed, and to assign them as atom attributes. Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc.
The tool is in the menu under Tools… Volume Data. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html
Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values. Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
The coloring could also be done with the “rangecolor” command, and labeling with “labelopt” (or menu Actions… Label… other). With labelopt you can specify a format so that you don’t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name:
labelopt info %(value_name_of_map).3f
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2015, at 1:33 PM, Noble, Alex ajn10d@fsu.edu wrote:
Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Alex,
You could get the interpolated density each atom position with the Values at Atom Positions dialog (menu Tools / Volume Data). Usually this is used to color the atoms based on density value, but the values can be written out with the Render by Attribute dialog menu File / Save Attributes.
It is not easy to see the positions of nearby grid points and those grid points can’t be selected. But if you really want to get at those values you might just display your map as a mesh and adjust the contour level by hand until you see the surface intersects a grid point (the contour lines in mesh mode lie in the grid planes so you may be able to visually see when the surface hits a grid point).
Tom
On Jan 30, 2015, at 1:33 PM, Noble, Alex ajn10d@fsu.edu wrote:
Hi all,
I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera?
Best, -Alex Noble _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Noble, Alex -
Tom Goddard