<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Dear Long Gui,<div class="">If you turn off both "rotation" and "shift" in the Fit in Map dialog (after showing Options) it is not supposed to move the atoms. You should probably get a newer version because 1.14 is quite old, but as far as I know that would not change this behavior. Nevertheless I did the test below in a much newer version, a 1.17 daily build. The most recent release of Chimera is 1.16 from December </div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/download.html" class="">https://www.rbvi.ucsf.edu/chimera/download.html</a>></div><div class="">...and I would expect it to behave the same as in my tests. Or, you could use ChimeraX instead, which has the same fitting capabilities and options as Chimera, although the command syntax and dialog appearance may be slightly different.</div><div class=""><br class=""></div><div class="">In Chimera 1.17:</div><div class="">I tested this by making a fake example of manually moving atomic model #1 near density calculated from some other model #0, and then entering values in the Fit in Map dialog and clicking the Update button. This worked correctly for me, meaning that the atomic model #1 did not move from where I put it. Here is an image of the settings in my dialog:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="F3E1E108-B216-44B5-9C95-B2D3619B93F3" width="581" height="296" src="cid:5B51DF11-E454-45EA-B99D-F5EC08C4B457" class=""></div><div class=""><br class=""></div><div class="">Alternatively, you can use the "measure correlation" command but only after the simulated map is created (either with the Fit in Map dialog as above, or with "molmap" command), because it requires specifying two maps:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation</a>></div><div class=""><br class=""></div><div class="">"molmap" command:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""></div><br class=""><blockquote type="cite" class="">On Feb 1, 2022, at 10:09 AM, Long Gui via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear Chimera-user group,<br class="">I am using Chimera version 1.14. After I have manually place the PDB model in the volume file, I would like to calculate the correlation value between the current position of PDB file and the volume. I have used "Fit dialog" and "use simulated map" but the correlation value only displayed the optimized value after shift and rotation. I have also disabled "rotation" and "shift" but the results were the same.<br class=""><br class="">Because my volume contains more proteins than the PDB files, the "Fit in map" always place the PDB files into the densities corresponding to other proteins. I just want to have the correlation value between the manually placed PDB and the volume. How could I do this in Chimera? <br class="">Thanks,<br class="">Long Gui, Ph.D. <br class=""></blockquote><br class=""></div></body></html>