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<div>Dear Tom,</div>
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<div>Thanks for the tip. Deleting the optional part of the script and rerunning it solves the problem!</div>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">Best regards,</font></font></div>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">Roman</font></font></div>
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<span style="font-weight:bold">From: </span>Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>><br>
<span style="font-weight:bold">Date: </span>Friday 30 October 2015 18:23<br>
<span style="font-weight:bold">To: </span>Roman Koning <<a href="mailto:r.i.koning@lumc.nl">r.i.koning@lumc.nl</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Chimera-users] resmap<br>
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Hi Roman,
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<div class=""> I tried ResMap and it produced a Chimera command script for my map emd_1007.map with file name</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>emd_1007_resmap_chimera.cmd</div>
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<div class="">That script tries to do both the surface coloring and the plane slicing animation. First it does the surface coloring, then it immediately shows only a single plane of the map so you can’t see the surface. So the script is messed up. If you
make a copy of the script, delete all the lines below the one that says OPTIONAL: ResMap Slice Animation, then start Chimera (with no data open) and open the new edited script it will show the colored surface. You would have to talk to the author of ResMap,
Alp Kucukelbir to get this fixed.</div>
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Tom</div>
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<div class="">Here is what the Chimera script produced by ResMap looks like for reference:</div>
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<div class=""># Color a map by local resolution computed by ResMap</div>
<div class=""># Initial version of script courtesy of Tom Goddard, UCSF.</div>
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<div class=""># Open both volumes and hide the ResMap volume.</div>
<div class="">set bg_color white</div>
<div class="">open #0 emd_1007.map</div>
<div class="">open #1 emd_1007_resmap.map</div>
<div class="">volume #1 hide</div>
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<div class=""># Color the original map with the values from the ResMap output.</div>
<div class="">scolor #0 volume #1 cmap 12.40,blue:14.42,cyan:16.44,green:18.46,yellow:20.48,orange:22.50,red:22.51,gray</div>
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<div class=""># OPTIONAL: ResMap Slice Animation.</div>
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<div class=""># Show midway slice of the original map with contour level below the minimum map value.</div>
<div class="">volume #0 planes z,65 step 1 level -1 style surface</div>
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<div class=""># Show a smooth transparent contour surface indicating the structure boundaries.</div>
<div class="">vop gaussian #0 sDev 5 model #2</div>
<div class="">volume #2 level 0.02 step 1 color .9,.7,.7,.5</div>
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<div class=""># Zoom out a bit and tilt to a nice viewing angle.</div>
<div class="">turn x -45</div>
<div class="">turn y -30</div>
<div class="">turn z -30</div>
<div class="">scale 0.5</div>
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<div class=""># Cycle through planes from N/2 to 4N/5 up to N/5 and back to N/2.</div>
<div class="">volume #0 planes z,65,104,0.25</div>
<div class="">wait 156</div>
<div class="">volume #0 planes z,104,26,0.25</div>
<div class="">wait 312</div>
<div class="">volume #0 planes z,26,65,0.25</div>
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<blockquote type="cite" class="">
<div class="">On Oct 30, 2015, at 8:24 AM, wrote:</div>
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<div style="" class="">I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input
map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the
resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. </div>
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<div class=""><font class="Apple-style-span"><font class="Apple-style-span" face="Calibri">Best regards,</font></font></div>
<div class=""><font class="Apple-style-span"><font class="Apple-style-span" face="Calibri"><br class="">
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<div class=""><font class="Apple-style-span"><font class="Apple-style-span" face="Calibri">Roman</font></font></div>
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