viewing grid density

Hello all, 1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same. 2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc. 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it. Bala

Hi Bala, (1) I do not understand your first question. If your PDB is saved from the same trajectory used to create the solvent density map, I would expect it to already be in the correct position relative to the map. I'm not sure what you mean by "fix" (freeze? or change its position relative to the map?). (2) the levels shown for the histogram are just the numbers present in your density map. The meaning of the numbers depends on the method you used to create the map, including grid spacing, number of trajectory frames used, and whether any normalization for atomic weight or number of frames was applied. You would need to look at the documentation for whatever you used to create the map. If you used MD Movie in Chimera to create this map, then the numbers are total counts of atoms in that cube of the grid summed over all the frames in the trajectory used for the calculation. This "occupancy analysis" in MD Movie is described here: http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/ movie.html#occupancy After you figure out the physical meaning of the numbers, there is still no rule as to what threshold to use, because it depends on the system and what degree of solvent localization you are trying to identify. Certain solute groups may localize water much more strongly than others. (3) a link and search interface to the chimera-users archive is included on this page http://www.cgl.ucsf.edu/chimera/docs/feedback.html Also "Help... Contact Us" in the Chimera menu opens a similar page. I hope this helps, Elaine On Oct 26, 2006, at 6:33 AM, bala wrote:
Hello all,
1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same.
2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc.
3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it.
Bala
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- 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

Hi Bala, Elaine Meng answered these questions before I finished my email. I think my answers are the same, but I'll give them to you anyways. If the solvent map and reference PDB structure produced by Amber8 do not align when displayed in Chimera that is probably a problem with Amber or how you are using Amber. If they do not align I do not think you will be able to align them in Chimera. The one thing you could try is to use volume dialog menu entry Features / Origin and Scale. That will show the grid plane spacing (called "voxel size") and the origin that is being used for the map. You can try changing those values by hand. Press the Enter key after changing a value to have the display updated. Chimera can compute solvent occupancy from a trajectory using its MD Movie tool. See the "occupancy analysis" section of the Chimera documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht... Perhaps this is an alternative way to do what you want. The threshold level in the Chimera volume dialog specifies what map value the contour surface is drawn at. The displayed surface goes through those points in space where the map has the specified value. What that means depends on what the values in your map mean. I don't know what the values in your solvent map computed by Amber8 mean. Here is the Chimera users list (found under the Contact Us link on the main Chimera web page): http://www.cgl.ucsf.edu/pipermail/chimera-users/index.html Tom
participants (3)
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bala
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Elaine Meng
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Thomas Goddard