[Chimera-users] viewing grid density

[Elaine Meng]

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
>
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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-----
Elaine C. Meng, Ph.D.                          meng at 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




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