<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yumeng,<div class=""><br class=""></div><div class=""> I would not expect any difference in the correlation coefficient between Windows and Linux or with a large map versus a small map.</div><div class=""><br class=""></div><div class=""> First the command you listed does not do any fitting since you use "shift false rotate false" which does not allow the model to move.</div><div class=""><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false</div><div><br class=""></div><div>So I assume you are doing this just to measure the correlation coefficient. And your output says the correlation coefficient is 0. That most likely means the atomic model is not located in the map. Why don't you just do the same steps in gui mode and see what happens -- it should produce exactly the same result as nogui mode. Also note that the displayed surface level matters because by default fitmap only uses data above the contour level of the displayed surface of the map you are fitting into. That actually may explain why your large map case did not work, because if you open a large map ChimeraX may initially just show a single plane in gray scale instead of a surface, and with no surface it won't have a surface level. So to get a predictable result you should use the volume command to show a surface of the full map and set the threshold level you want to use, for example,</div><div><br class=""></div><div> volume #1 style surface region all level 0.2</div><div><br class=""></div><div> I see that ChimeraX does not have the "measure correlation" command that is in the older Chimera program. I will try to add that.</div><div><br class=""></div><div> Tom</div><div><br class=""></div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 10, 2022, at 2:14 PM, Yumeng Yan via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">When I tried to use<b class=""> fitmap</b> function ChimeraX in<span class="Apple-converted-space"> </span><b class="">Linux with --nogui option, </b><span class="Apple-converted-space"> </span>I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this<span class="Apple-converted-space"> </span><span class="">situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me?</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""><br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Here are the commands:</span></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""></span></p><div class="">open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb</div><div class="">fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false</div><div class=""><br class=""></div>Here is the log information:<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><p style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""></span></p><div class="">INFO:</div><div class="">UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)</div><div class="">INFO:</div><div class="">© 2016-2021 Regents of the University of California. All rights reserved.</div><div class="">INFO:</div><div class="">Executing: open .33092SymAndFit.cxc</div><div class="">INFO:</div><div class="">Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80%</div><div class="">STATUS:</div><div class="">reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87%</div><div class="">STATUS:</div><div class="">Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc</div><div class="">STATUS:</div><div class="">Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc</div><div class="">STATUS:</div><div class="">Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292</div><div class="">STATUS:</div><div class="">Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles</div><div class="">INFO:</div><div class="">Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32</div><div class="">INFO:</div><div class="">Chain information for fit_11.pdb #2</div><div class="">---</div><div class="">Chain | Description</div><div class="">[F](cxcmd:select /F:2-219 "Select chain") | [No description</div><div class="">available](cxcmd:sequence chain #2/F "Show sequence")</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">INFO:</div><div class="">Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false</div><div class="">INFO:</div><div class="">Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32</div><div class="">INFO:</div><div class="">Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points</div><div class=""> correlation = 0, correlation about mean = 0, overlap = 0</div><div class=""> steps = 24, shift = 0, angle = 0 degrees</div><div class=""><br class=""></div><div class="">INFO:</div><div class="">Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates:</div><div class=""> Matrix rotation and translation</div><div class=""> 1.00000000 0.00000000 0.00000000 0.00000000</div><div class=""> 0.00000000 1.00000000 0.00000000 0.00000000</div><div class=""> 0.00000000 0.00000000 1.00000000 0.00000000</div><div class=""> Axis 0.00000000 0.00000000 1.00000000</div><div class=""> Axis point 0.00000000 0.00000000 0.00000000</div><div class=""> Rotation angle (degrees) 0.00000000</div><div class=""> Shift along axis 0.00000000</div><div class=""><br class=""></div><div class="">STATUS:</div><div class="">24 steps, shift 0, rotation 0 degrees, correlation 0.0000</div><div class=""><br class=""></div><br class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Best wishes, </span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Yumeng</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><p class="x_MsoNormal" style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif; color: rgb(33, 33, 33); line-height: 8pt;"><span lang="EN-US" style="font-size: 7.5pt; font-family: Verdana, sans-serif, serif, EmojiFont; color: gray;" class=""></span></p><div style="color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; 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