<div dir="ltr"><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Thank you very much, Eric. Unhappily I am not familiar with Python scripting, so I will have to wait that someone with that skill adds this useful tool into Chimera code!</span><br></div><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">But for now I will take Elaine's hints!</span></div><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Thank you again</span></div><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Sergio</span></div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jul 31, 2018 at 3:38 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space">Hi Sergio,<div><span class="m_-3433718881312300701Apple-tab-span" style="white-space:pre-wrap"> </span>If you are comfortable writing Python code, there is a provision for adding custom header types to Multalign Viewer. Look at the MAVHeader module in your Chimera distribution (<your Chimera>/share/MAVHeader), particularly the file ChimeraExtension.py which defines headers for charge variation and CA/backbone/full RMSDs and registers those headers with Multalign Viewer. I imagine you will have questions (LOL!) so I have directed responses to the chimera-dev mailing list, which would seem more appropriate in this case.</div><div><br></div><div>—Eric</div><div><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><span class="m_-3433718881312300701Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div><span class="m_-3433718881312300701Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div><br></div></div>
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<div><br><blockquote type="cite"><div>On Jul 31, 2018, at 11:22 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:</div><br class="m_-3433718881312300701Apple-interchange-newline"><div><div style="word-wrap:break-word;line-break:after-white-space">Hi Sergio,<div>Sorry, there isn’t a way to automatically make residue attributes into a header. We had imagined that people would be calculating properties outside of Chimera, and then using a script or even manually creating a file in the header format to load them as a header.</div><div><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat</a>></div><div><br></div><div>However, you can change the sequence lettering colors to match the ribbon, so if you first colored ribbon by some residue attribute (with Render by Attribute or command “rangecolor”), it could be reflected back into the sequence window in that way. To do that, use sequence window menu Preferences… Appearance, and then for residue letter coloring (near the bottom), choose “coloring scheme: ribbon”. I realize this might not be optimal if some of the coloring makes the letters hard to read. </div><div><br></div><div>I attached an example image with my protein colored by residue average bfactor (blue -> red -> yellow) and using “ribbon” coloring of the associated sequence in the alignment.</div><div><br></div><div>With a header you could only have one value per column, but with ribbon coloring you could have different values (colors) in the same column if there are multiple structures associated.</div><div><br></div><div>I hope this helps,</div><div>Elaine<br><div>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Chimera(X) team<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><span id="m_-3433718881312300701cid:BEFE45F4-30BF-4513-AD82-E926BDF34795@cgl.ucsf.edu"><Screen Shot 2018-07-31 at 11.18.18 AM.png></span><br><br></div><br><blockquote type="cite">On Jul 31, 2018, at 6:05 AM, Sergio Garay <<a href="mailto:sergio.alberto.garay@gmail.com" target="_blank">sergio.alberto.garay@gmail.com</a>> wrote:<br><br>Hi All!<br><br>I would like to know:<br>Is there any way or tool to write some calculated attribute into a header format?<br><br>I want to see the same color values obtained for some a calculated attribute projected onto a sequence.<br><br>I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. <br><br>Thank you in advance.<br><br>-- <br>Sergio Garay<br>Dr. en Ciencias Biológicas<br>Facultad de Bioquimica y Cs. Biológicas<br>Universidad Nacional del Litoral<br>Santa Fe - Argentina<br>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br>Argentina<br>Ph. +54 (342) 4575-213<br>Fax. +54 (342) 4575-221<br>_______________________________________________<br>Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><br></div></div>_______________________________________________<br>Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><font color="#0000ff" size="1"><i>Sergio Garay<br>Dr. en Ciencias Biológicas<br>Facultad de Bioquimica y Cs. Biológicas<br>Universidad Nacional del Litoral<br>Santa Fe - Argentina<br>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br>Argentina<br>Ph. +54 (342) 4575-213<br>Fax. +54 (342) 4575-221 </i></font></div></div></div>