<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p>Hi, </p>
<p><br>
</p>
<p>When I tried to use<b> fitmap</b> function ChimeraX in <b>Linux with --nogui option, </b> I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this
<span>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></p>
<p><span><br>
</span></p>
<p><span>Here are the commands:</span></p>
<p><span></p>
<div>open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb</div>
<div>fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false</div>
<div><br>
</div>
Here is the log information:</span>
<p></p>
<p><span></p>
<div>INFO:</div>
<div>UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)</div>
<div>INFO:</div>
<div>© 2016-2021 Regents of the University of California. All rights reserved.</div>
<div>INFO:</div>
<div>Executing: open .33092SymAndFit.cxc</div>
<div>INFO:</div>
<div>Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80%</div>
<div>STATUS:</div>
<div>reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87%</div>
<div>STATUS:</div>
<div>Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc</div>
<div>STATUS:</div>
<div>Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc</div>
<div>STATUS:</div>
<div>Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292</div>
<div>STATUS:</div>
<div>Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles</div>
<div>INFO:</div>
<div>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>INFO:</div>
<div>Chain information for fit_11.pdb #2</div>
<div>---</div>
<div>Chain | Description</div>
<div>[F](cxcmd:select /F:2-219 "Select chain") | [No description</div>
<div>available](cxcmd:sequence chain #2/F "Show sequence")</div>
<div><br>
</div>
<div><br>
</div>
<div>INFO:</div>
<div>Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false</div>
<div>INFO:</div>
<div>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>INFO:</div>
<div>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> correlation = 0, correlation about mean = 0, overlap = 0</div>
<div> steps = 24, shift = 0, angle = 0 degrees</div>
<div><br>
</div>
<div>INFO:</div>
<div>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> Matrix rotation and translation</div>
<div> 1.00000000 0.00000000 0.00000000 0.00000000</div>
<div> 0.00000000 1.00000000 0.00000000 0.00000000</div>
<div> 0.00000000 0.00000000 1.00000000 0.00000000</div>
<div> Axis 0.00000000 0.00000000 1.00000000</div>
<div> Axis point 0.00000000 0.00000000 0.00000000</div>
<div> Rotation angle (degrees) 0.00000000</div>
<div> Shift along axis 0.00000000</div>
<div><br>
</div>
<div>STATUS:</div>
<div>24 steps, shift 0, rotation 0 degrees, correlation 0.0000</div>
<div><br>
</div>
<br>
</span>
<p></p>
<p><span>Best wishes, </span></p>
<p><span>Yumeng</span></p>
<p><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<p></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"></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; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><b>Yumeng Yan</b></span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
Postdoctoral Fellow </span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
</span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
</span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><b>Taylor and R<span>asmussen</span> Group</b></span></font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><b>University of Copenhagen</b></span></font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt">Faculty of Health and Medical Sciences</span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><b><br>
</b></span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt">Novo Nordisk Foundation Center for Protein Research</span></font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
Blegdamsvej 3B, building 6</span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
2200 Copenhagen N</span></font><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><br>
DENMARK</span></font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<br>
</div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><span style="font-size:7.5pt"><a href="mailto:yumeng.yan@cpr.ku.dk" class="OWAAutoLink" id="LPNoLP">yumeng.yan@cpr.ku.dk</a></span></font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><br>
</font></span></font></div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px; margin:0px">
<font size="3" style="font-family:Calibri,sans-serif,serif,EmojiFont"><span style="font-size:12pt"><font size="1" color="gray" style="font-family:Verdana,sans-serif,serif,EmojiFont"><img class="EmojiInsert" alt="1638361915486" style="" src="cid:ccddf43b-cbbe-4084-ba85-4256acbdac26"><br>
</font></span></font></div>
<p class="x_MsoNormal" style="margin:0cm; font-size:12pt; font-family:Calibri,sans-serif; color:rgb(33,33,33)">
<span lang="EN-US" style="font-size:7.5pt; font-family:Verdana,sans-serif,serif,EmojiFont; color:gray"></span></p>
<p></p>
</div>
</div>
</div>
</body>
</html>