<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Daniel,<div class="">Something you and other ChimeraX users may be interested in is that you can fetch the UniProt sequence and then view the sequence features on both the sequence and the associated structure. There are several types of sequence features, but "modified residue" is one of them. So for your purposes, I guess it depends on how well UniProt has annotated the sequence with its known modified sites, how often updated from the literature, etc.</div><div class=""><br class=""></div><div class="">Maybe the least convenient step for this currently is that you need to look up the UniProt ID of the chain of interest. The simplest may be to look it up at the RCSB PDB website. I couldn't think of a nice way using ChimeraX alone (blast nr takes too long).</div><div class=""><br class=""></div><div class="">So I can open 1i10 and the corresponding UniProt sequence, according to the entry for that structure in the RCSB PDB:</div><div class=""><<a href="http://www.rcsb.org/structure/1I10" class="">http://www.rcsb.org/structure/1I10</a>></div><div class=""><br class=""></div><div class="">open 1i10</div><div class="">open uniprot:p00338</div><div class=""><br class=""></div><div class="">... in ChimeraX, that automatically pops up a dialog listing the uniprot sequence features. Choosing some feature automatically shows it as colored boxes on the sequence and selects the corresponding positions on the structure. In the attached images I just chose all "modified residue" features in the left side of the features table, but if you wanted to get more specific and just see for example the phosphotyrosine site, you could choose that on the right side of the features table.</div><div class=""><br class=""></div><div class="">Here's the User Guide info on viewing UniProt features in ChimeraX:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><img apple-inline="yes" id="72A21025-090A-4494-A0A4-E97415D082A3" width="599" height="671" src="cid:623F6790-E360-4A1F-BA3B-97647C64685A@gateway.sonic.net" class=""><img apple-inline="yes" id="CD4BB9F6-A3D6-42DB-B140-29E1D2FA6D49" width="637" height="165" src="cid:B1EBAFA9-96CA-44C7-B501-37582DAA725D@gateway.sonic.net" class=""><img apple-inline="yes" id="FF3C9F26-9067-4707-B093-4399D1EDACE9" width="350" height="571" src="cid:A6C7B2CE-A6B6-47DA-B0F5-3317BFEF7F42@gateway.sonic.net" class=""></div><br class=""><blockquote type="cite" class="">On Feb 23, 2021, at 11:15 AM, Daniel Gurnon <<a href="mailto:danielgurnon@depauw.edu" class="">danielgurnon@depauw.edu</a>> wrote:<br class=""><br class="">Thanks for the quick feedback Eric and Elaine.<br class=""><br class="">I only stumbled upon this this morning while thinking how nice it would be to be able to highlight all post-translational modification sites in a protein, to compare with variants of uncertain significance....I did a google search to see if something like that already existed, and at first glance this PSP script seemed to be the answer. But now it seems like it would be easier to write my own script. <br class=""><br class="">____________________________<br class=""><br class="">Daniel Gurnon, Ph. D.<br class="">Associate Professor of Chemistry and Biochemistry<br class="">DePauw University<br class="">Greencastle, IN 46135<br class=""><br class=""><br class="">On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class="">Hi Daniel,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The script will actually execute if you wait several minutes. The problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.<br class=""><br class="">--Eric<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Feb 23, 2021, at 9:06 AM, Daniel Gurnon <danielgurnon@depauw.edu> wrote:<br class=""><br class="">Hi all,<br class="">I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:<br class=""><br class="">Here's an example of a page with an available Chimera script. From what I read in the documentation about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.<br class=""><br class="">When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error<br class=""><br class="">setattr a label Ser-89 :88.A@OG<br class="">Expected a keyword<br class=""><br class="">Thanks in advance for the assistance,<br class="">Dan<br class="">____________________________<br class=""><br class="">Daniel Gurnon, Ph. D.<br class="">Associate Professor of Chemistry and Biochemistry<br class="">DePauw University<br class="">Greencastle, IN 46135<br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class="">ChimeraX-users@cgl.ucsf.edu<br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></blockquote><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class="">ChimeraX-users@cgl.ucsf.edu<br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></blockquote><br class=""></div></body></html>