<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Sep 7, 2012, at 1:19 PM, Daniel Gurnon wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi everyone,<div><br></div><div>To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script:</div>
<div><br></div><div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0in; margin-left: 0in; font-family: Calibri; font-size: 11pt; ">mm #0 #1 show true</div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0in; margin-left: 0in; font-family: Calibri; font-size: 11pt; ">rangecolor mavRMSD
min white mid pink max red</div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0in; margin-left: 0in; font-family: Calibri; font-size: 11pt; "><br></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0in; margin-left: 0in; font-family: Calibri; font-size: 11pt; "><br></div></div><div>This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window?</div></blockquote></div><div><br></div><div>Hi Dan,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>The way Chimera is currently structured, there is no way to get that RMSD attribute assignment without creating the MAV window. Now I <i>could</i> give you a script that closes the open MAV windows, which you could insert into your per-frame commands, but if I'm going to give you a script I might as well give you one that entirely bypasses the matchmaker/mav steps (which do a lot more work than strictly necessary for your purposes). I've attached such a script. Assuming you saved that script into the "Documents" folder of your home directory, your per-frame command would change to:</div><div><br></div><div><div>runscript ~/Documents/md-rmsd.py</div><div>rangecolor trajRMSD min white mid pink max red</div><div><br></div><div>As you might surmise from the rangecolor command above the script defines a "trajRMSD" attribute. Also, I think you want to use actual specific numeric values rather than min/mid/max, since even matching against the reference frame can produce small numeric differences (due to PDB precision roundoff) which will nonetheless look just as big as much larger differences elsewhere in the trajectory.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Now, I'm not certain for what purpose you are making this RMSD depiction, but I thought I should point out that in the daily build you can plot the RMSD difference for any set of atoms in a particular frame against the rest of the trajectory. That feature is in MD Movie's Analysis->Plot menu.</div><div><br></div><div>--Eric</div><div><br></div><div><br></div><div><br></div></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: 16px; 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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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