Electron density map around selected residues
Hello - I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera? Thanks - Miles Miles Pufall UC San Francisco
Hi Miles, You can use the zone tool in the volume viewer (Features->Zone), it works great for depicting the electron density for a given area. I first hide the density by clicking on the eyeball in the volume viewer, then select the residues I want and click the zone button. Clicking the eyeball again shows the density in only the selected zone. You can give a zone radius too. -Wally On Jul 23, 2008, at 3:32 AM, Miles Pufall wrote:
Hello -
I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera?
Thanks -
Miles
Miles Pufall UC San Francisco
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
Hi Miles, Sure, you can limit the display to a zone around selected atoms. In Volume Viewer, choose Features... Zone. Select the atoms, click Zone. You can then move the slider to change the zone radius. This affects the "active" data set, the one with the highlighted name in the Volume Viewer dialog. If you have more than one density map, just click on the histogram for the other one to make it the active set and click Zone again. The only tricky thing is that moving the slider only adjusts one zone at a time, but you can switch back and forth by clicking the histograms. It is fine to deselect the atoms - it "remembers" which atoms were selected when you clicked Zone. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume... I know you work in the same building as we do - feel free to stop by my office if any of this is unclear! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 23, 2008, at 12:32 AM, Miles Pufall wrote:
Hello -
I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera?
Thanks -
Miles
Miles Pufall UC San Francisco
participants (3)
-
Elaine Meng -
Miles Pufall -
Walter Novak