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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Eric/Elaine,<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">That’s perfect thanks – just what I needed to know!<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>
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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>Thursday, 23 January 2020 at 18:46<br>
<b>To: </b>"chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
<b>Cc: </b>"Healey, Joseph" <J.Healey.1@warwick.ac.uk><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">Like Elaine says, skipping the assignment entirely is perfectly acceptable. If it’s easier to assign something than skip it, assign None.
<o:p></o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<span class="apple-tab-span"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Eric Pettersen<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">UCSF Computer Graphics Lab<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal">On Jan 23, 2020, at 10:03 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Joe,<br>
Maybe I’m misunderstanding the issue, but can’t you just skip assigning a value to that residue if it does not have a score? That would be the same as omitting the residue from an attribute assignment file.<br>
<br>
It depends how you want to use the attribute: do you want those residues to have the attribute but assigned as none, or do you want them simply not to have that attribute?<br>
<br>
An analogous situation is the amino acid hydrophobicity attribute. The following command-line specifier designates residues (such as water or nucleic acids) that lack a Kyte-Doolittle hydrophobicity assignment:<br>
<br>
:/^kdHydrophobicity <br>
<br>
… and the Render by Attribute tool and rangecolor command both have options as to what you want to do with such “no-value” atoms or residues.<br>
<br>
To summarize, you may not need to assign some kind of null value, but simply skip assigning anything.<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On Jan 23, 2020, at 2:51 AM, Healey, Joseph <<a href="mailto:J.Healey.1@warwick.ac.uk">J.Healey.1@warwick.ac.uk</a>> wrote:<br>
<br>
Hi Chimera team,<br>
<br>
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?<br>
<br>
e.g. if I have the structure sequence, and the scores (just using integers as a simple example for now):<br>
model.residues = MEREYV<br>
Scores = 192984<br>
<br>
I can assign those scores reasonable easily as discussed with something to the effect of:<br>
<br>
for res, score in zip(model.residues, scores):<br>
setattr(res, “attributeName”, score)<br>
<br>
If in the case I have scores with missing data however, what value for missing is acceptable/expected by chimera (“”, None etc)?<br>
<br>
E.g:<br>
Scores = 192-84<br>
<br>
In which case I envisage doing something like:<br>
<br>
for res, score in zip(model.residues, scores):<br>
if score == “-“:<br>
setattr(res, “attributeName, “”) # Or whatever the allowable character/value is?<br>
else:<br>
setattr(res, “attributeName”, score)<br>
<br>
Many thanks,<br>
<br>
Joe<o:p></o:p></p>
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