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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Chimera team,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I’ve made some good headway with the subject of this previous thread (a relatively simple Bio.pairwise2 alignment approach seems to serve to associate chains reasonably well. One further thing I’d
like to clarify, is how missing data is stored for a residue attribute in the case of the renderbyattribute functionality?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">e.g. if I have the structure sequence, and the scores (just using integers as a simple example for now):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">model.residues = MEREYV<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Scores = 192984<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I can assign those scores reasonable easily as discussed with something to the effect of:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">for res, score in zip(model.residues, scores):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> setattr(res, “attributeName”, score)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">If in the case I have scores with missing data however, what value for missing is acceptable/expected by chimera (“”, None etc)?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">E.g:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Scores = 192-84<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">In which case I envisage doing something like:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">for res, score in zip(model.residues, scores):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> if score == “-“:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> setattr(res, “attributeName, “”) # Or whatever the allowable character/value is?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> else:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> setattr(res, “attributeName”, score)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Joe<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Serif Roman";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><u><span style="font-size:10.0pt;font-family:"CMU Serif Roman";color:black">
<o:p></o:p></span></u></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:#941100">Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB</span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:#941100"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">Research Fellow<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">Warwick Medical School</span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">University of Warwick</span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">Coventry</span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">CV47AL<br>
Mob: +44 (0) 7536 042620 | Twitter: <a href="https://twitter.com/JRJHealey"><span style="color:#0563C1">@JRJHealey</span></a> | </span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:black"><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey"><span style="font-size:10.0pt;color:#0563C1">Website</span></a><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"CMU Sans Serif Medium";color:black">Email:
<a href="mailto:J.Healey.1@warwick.ac.uk"><span style="color:#0563C1">J.Healey.1@warwick.ac.uk</span></a> | ORCID: orcid.org/0000-0002-9569-6738</span><span style="font-size:12.0pt;font-family:"CMU Sans Serif Medium";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Reply to: </b>"chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
<b>Date: </b>Wednesday, 4 December 2019 at 01:00<br>
<b>To: </b>"Healey, Joseph" <J.Healey.1@warwick.ac.uk><br>
<b>Cc: </b>"chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [Chimera-users] Auto-associate define attribute/render by attribute<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Dec 3, 2019, at 1:15 AM, Healey, Joseph <<a href="mailto:J.Healey.1@warwick.ac.uk">J.Healey.1@warwick.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<li class="MsoListParagraph" style="mso-list:l0 level1 lfo1">On a related note, is there a need to programmatically ‘refresh’ rangecol/RBA after defining the attribute, as there is with the dialogue box, or should it be happy once the attr is set?<o:p></o:p></li></ol>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">rangecolor will work without any nudging. The Render By Attribute dialog will remain blissfully unaware of the new attributes until you use its refresh menu item. You can use that dialog’s refreshAttrs() method to programatically nudge
it. Look at MultAlignViewer/MAViewer.py in your Chimera distribution for an example (search for refreshAttrs).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<span class="apple-tab-span"><o:p></o:p></span></p>
<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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