<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference.</div><div class=""><br class=""></div><div class="">I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I’d like to render these ranges of residues semitransparent. I’ve tried to do this with the transparency command but this applies to ribbons only (I think). </div><div class=""><br class=""></div><div class="">I’d appreciate any suggestions as to how this can be done. </div><div class=""><br class=""></div><div class="">Thank you in advance</div><div class=""><br class=""></div><div class="">George</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="40D54B59-E0F7-43C3-B70D-01FF3E6C873F" height="925" width="1041" apple-width="yes" apple-height="yes" src="cid:37B6BE05-3653-4A15-948B-AE3C3CBB2ACA" class=""></div><div class=""><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>></div><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">Subject: coloring by RMSD (conformational variability)</div><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">Date: 25 March 2014 at 19:32:47 GMT+1</div><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">To: George Tzotzos <<a href="mailto:gtzotzos@me.com" class="">gtzotzos@me.com</a>></div><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">Cc: chimera List <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>></div><div style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue';" class="">Reply-To: "<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">Hi George,</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work:</span></div><div style="margin: 0px; line-height: normal; min-height: 25px;" class=""><span style="font-kerning: none" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">(1) show the sequence (menu: Favorites… Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence.</span></div><div style="margin: 0px; line-height: normal; min-height: 25px;" class=""><span style="font-kerning: none" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">(2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure… Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence.</span></div><div style="margin: 0px; line-height: normal; min-height: 25px;" class=""><span style="font-kerning: none" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">(3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers… RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low.</span></div><div style="margin: 0px; line-height: normal; min-height: 25px;" class=""><span style="font-kerning: none" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">(4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools… Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets… Publication 1) in the attached image.</span></div><div style="margin: 0px; line-height: normal; min-height: 25px;" class=""><span style="font-kerning: none" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">I hope this helps,</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-kerning: none" class="">Elaine</span></div></div></body></html>