<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Thanks Elaine-<div><br></div><div>My structures have more than 20 individual components (recent spliceosome cryo-EM models- example PDB 5GMK). They came as 1 model, which I split to have more control over for analysis. I can go through each component by hand and copy/paste the color for each model into a text file and then turn then this into a command file to color another structure with the same components in another conformation. (Thanks for turning me on to the “modelcolor” command. That will be helpful!) However, I was hoping there was a way to use something like grep to extract this information from the .py session file.</div><div><br></div><div>Melissa</div><div><br></div><div><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><span class="Apple-style-span" style="border-collapse: separate; font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><i><p style="font-family: GillSans-SemiBoldItalic; margin: 0px;"><font style="font-variant: normal; line-height: normal;">^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Melissa S. Jurica, Ph.D.</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Professor, </font><span style="text-align: -webkit-auto;">Molecular, Cell & Developmental Biology</span></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Center for Molecular Biology of RNA</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">University of California, Santa Cruz</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">1156 High Street</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Santa Cruz, CA 95064</font></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px; font-variant: normal; line-height: normal; min-height: 14px;"><br></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Office: 450 Sinsheimer Labs<span class="Apple-tab-span" style="white-space: pre;"> </span></font>Lab: 434 Sinsheimer Labs </p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><font style="font-variant: normal; line-height: normal;">Office phone (831) 459-4427<span class="Apple-tab-span" style="white-space: pre;"> </span></font><span style="text-align: -webkit-auto;">Lab phone (831) 459-2463<span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="text-align: -webkit-auto;">Fax (831) 459-3139</span></p><p style="font-family: GillSans-SemiBoldItalic; font-weight: bold; margin: 0px;"><span style="text-align: -webkit-auto;"><a href="http://www.mcd.ucsc.edu/faculty/jurica.html">http://www.mcd.ucsc.edu/faculty/jurica.html</a></span></p><p style="margin: 0px;"><span style="text-align: -webkit-auto;"><font face="Gill Sans">^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^</font></span></p></i></div></span></div></span></div></div></div></div></div></div></div>
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<br><div><div>On Sep 2, 2016, at 5:11 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Melissa,<br>At first I was going to suggest “mcopy” but from your description, it sounds like you have each chain as a separate model. “mcopy” is only for copying settings within one model to other models.<br><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html</a>><br><br>You can get the current atom-color RGB definitions or hex codes by Ctrl-click to select an atom (or ribbon segment to select the whole residue, if all of its atoms are the same color), showing the Selection Inspector, Inspect: atom, and then clicking the square color well to get the Color Editor. Then in the Color Editor you can see the hex code starting with # in the “Color name” field.<br><br>The square in the Model Panel shows the model-level color. Chimera has a coloring hierarchy, where if the atoms are individually assigned colors (such as with your color command), in the 3D display those colors mask the model-level color, which may be different. You can use the modelcolor command, for example “modelcolor #6168c8fb41bc #0.17” or click the color square in the Model Panel to make the Color Editor dialog appear, and then enter the hex code in the “Color name” field of the Color Editor: <br><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html</a>><br>There is only one model-level color per model, as the name suggests, even though the atoms and per-residue ribbon segments might be all different colors.<br><br>More about color hierarchy:<br><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html</a>><br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br>On Sep 2, 2016, at 1:23 PM, Melissa Jurica <<a href="mailto:mjurica@ucsc.edu">mjurica@ucsc.edu</a>> wrote:<br><br><blockquote type="cite">I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations?<br><br>For example:<br><br>color #6168c8fb41bc #0.17<br><br>Also-<br>How do I get that color to apply to the little square that shows up on the model panel?<br><br>Melissa<br></blockquote><br></blockquote></div><br></div></body></html>