<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">As long as we are talking about exact (sub)sequence matches, I think it is reasonably simple to do in Python:<div class=""><br class=""></div><div class=""># pairs of sequences and corresponding values you want to assign…</div><div class="">seq_vals = [</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>(“ADTY…whatever…PLHE”, (1.97, 2.14, … same len as sequence…, 0.88, 1.22)),</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>(“…next sequence…”, (…next set of values…))</div><div class="">]</div><div class="">from chimera import openModels, Molecule</div><div class="">for m in openModels.list(modelTypes=[Molecule]):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for seq in m.sequences():</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for target_seq, vals in seq_vals:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>try:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>i = str(seq).index(target_seq)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>except ValueError:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>continue</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for offset, val in enumerate(vals):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>r = seq.residues[i+offset]</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>if r:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>r.chouFasmanImmuno = val</div><div class=""><br class=""></div><div class="">A few notes:</div><div class=""><br class=""></div><div class="">1) If there is missing structure, there maybe not be a residue that corresponds to a sequence position, which is why there is an “if r:” test in the script. The full sequence is known from the SEQRES records in the PDB file.</div><div class=""><br class=""></div><div class="">2) Avoid assigning an attribute name starting with an upper-case letter. Symbolic constants start with upper-case letters and the render-by-attr code will screen out such attributes from its interface. There is a way around this by registering the attribute with the SimpleSession module (which will also get the attribute to save in sessions). I can provide details if needed.</div><div class=""><br class=""></div><div class="">3) You may want to read the sequences and values from a file rather than have them directly in the script. You might also want to set multiple attributes, in which case you would include the the attribute name along with the sequence and values, and change the corresponding ‘for’ loop and change ‘r.attrName = val’ to setattr(r, attrName, val). I don’t know how good your Python juju is, but I can provide guidance as needed.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 29, 2019, at 8:22 AM, Healey, Joseph <<a href="mailto:J.Healey.1@warwick.ac.uk" class="">J.Healey.1@warwick.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Hi Eric,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">I’ve been giving this some more thought. Is there perhaps a way to brute force this?<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">My thinking at the moment is, given that I’ll know the sequence, positions, and scores I want to use, all I really need to do is somehow set the attributes of the relevant object, perhaps circumventing MAV altogether? My main question is then, how are attributes for the models currently stored? Does `mavAttributeName` become an actual attribute of the `molecule.residue[n]`?<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Broadly I was thinking something like this might work based on your code suggestion below:<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><ul type="disc" style="margin-bottom: 0cm; margin-top: 0cm;" class=""><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt -15.75pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="">Split the open model to get individual models for the chains<o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt -15.75pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="">Iterate the list of models, and test whether their .sequence() matches the sequence I expect (perhaps via alignment if not perfect matches). I could read the attribute file in alongside this in base python, which perhaps means I don’t need to use the defined format too, and therefore can encode the seq/score/position all in one go.<o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt -15.75pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="">If it does, assign the relevant attribute name/score to the residue/model (depending on how exactly the attributes are stored at the moment). As simple as Molecule.Residue.mavAttributeName? Though of course there wouldn’t necessarily need to be a “mav” in there.<o:p class=""></o:p></span></li><ul type="circle" style="margin-bottom: 0cm; margin-top: 0cm;" class=""><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt -15.75pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="">If not, move on to the next model<o:p class=""></o:p></span></li></ul><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt -15.75pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="">If I can ‘force’ the attributes on to the residues etc, I can then trigger the rendering without needed to use MAV?<o:p class=""></o:p></span></li></ul><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Presumably there’s a way to ‘inject’ the namespace with an object equivalent to that which MAV/DefineAttribute would achieve, and I can do the association ‘manually’?<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Many thanks,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Joe<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Serif Roman";" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><u class=""><span style="font-size: 10pt; font-family: "CMU Serif Roman";" class=""> <o:p class=""></o:p></span></u></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium"; color: rgb(148, 17, 0);" class="">Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB</span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium"; color: rgb(148, 17, 0);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">Research Fellow<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">Warwick Medical School</span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium";" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">University of Warwick</span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium";" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">Coventry</span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium";" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">CV47AL<br class="">Mob: +44 (0) 7536 042620 | Twitter: <a href="https://twitter.com/JRJHealey" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">@JRJHealey</span></a> | </span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium";" class=""><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 10pt; color: rgb(5, 99, 193);" class="">Website</span></a><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "CMU Sans Serif Medium";" class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:J.Healey.1@warwick.ac.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">J.Healey.1@warwick.ac.uk</span></a><span class="Apple-converted-space"> </span>| ORCID: <a href="http://orcid.org/0000-0002-9569-6738" style="color: purple; text-decoration: underline;" class="">orcid.org/0000-0002-9569-6738</a></span><span style="font-size: 12pt; font-family: "CMU Sans Serif Medium";" class=""><o:p class=""></o:p></span></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Reply to:<span class="Apple-converted-space"> </span></b>"<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Wednesday, 27 November 2019 at 23:56<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"<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>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b>"Healey, Joseph" <<a href="mailto:J.Healey.1@warwick.ac.uk" class="">J.Healey.1@warwick.ac.uk</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [Chimera-users] Auto-associate define attribute/render by attribute<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Nov 27, 2019, at 1:07 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">meng@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">Python is beyond my skill set, though… somebody else would have to advise on that.<o:p class=""></o:p></span></div></div></div></blockquote></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The first thing I should say is that Multalign Viewer is only available as a graphical tool, so you will only be able to script this for a Chimera that is running its graphical interface, not in any headless “batch” mode. Okay, with that out of the way, the first job is to get a Python instance of Multalign Viewer showing the sequence you want with the chains you want associated. Unlike ChimeraX, which associates on a per-chain basis, Chimera associates on a per-structure basis, so you will have to first split your structure apart by chains (with the “split” command). If you have the pertinent sequence in a file, you could do this:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">from MultAlignViewer.MAViewer import MAViewer<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">mav = MAViewer(“full-path-to-sequence-file”)<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">If you don’t have a file, but you know you want to use the sequence of chain C, you could do this:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">from chimera import openModels, Molecule<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">for m in openModels.list(modelTypes=[Molecule]):<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">try:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">seq = m.sequence(‘C’)<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">except KeyError:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">continue<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">from MultAlignViewer.MAViewer import MAViewer<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">mav = MAViewer([seq])<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">You then add your custom header file with:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">mav.readHeaderFile(“full-path-to-header-file”)<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">After that, the residues will have the necessary attribute (prefixed with “mav”, so if the header attribute is ChouFasmanImmuno, the residue attribute is mavChouFasmanImmuno).<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">—Eric<o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><span class="apple-tab-span"><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Eric Pettersen<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">UCSF Computer Graphics Lab<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; 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