<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Bala,<DIV>(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?).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>(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:</DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/movie.html#occupancy">http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/movie.html#occupancy</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>(3) a link and search interface to the chimera-users archive is included on this page</DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/docs/feedback.html">http://www.cgl.ucsf.edu/chimera/docs/feedback.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Also "Help... Contact Us" in the Chimera menu opens a similar page.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I hope this helps,</DIV><DIV>Elaine</DIV><DIV><BR><DIV><DIV>On Oct 26, 2006, at 6:33 AM, bala wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P><FONT size="2">Hello all,<BR> <BR> 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.<BR> <BR> 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.<BR> <BR> 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it.<BR> <BR> Bala<BR> </FONT> </P><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----</DIV><DIV>Elaine C. Meng, Ph.D. <A href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</A></DIV><DIV>UCSF Computer Graphics Lab and Babbitt Lab</DIV><DIV>Department of Pharmaceutical Chemistry</DIV><DIV>University of California, San Francisco</DIV><DIV> <A href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>