<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="">Hi Arun,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Thanks for pointing this out. I have fixed the problem in the script on the <a href="https://rbvi.github.io/chimerax-recipes/" class="">ChimeraX Recipes</a> site. Use that one.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 9, 2021, at 1:16 AM, Gupta, Arun <<a href="mailto:Arun.Gupta@warwick.ac.uk" class="">Arun.Gupta@warwick.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.693333625793457px; font-size: 11pt; font-family: Calibri, sans-serif; text-align: justify;"><span style="background-color: white; font-family: Calibri, Helvetica, sans-serif;" class="">That' really great Eric. Also, Recently I have noticed that previous version of the script worked wonderfully for the proteins, which have both the secondary structural elements in the protein structure i.e </span><span style="font-family: Calibri, Helvetica, sans-serif;" class="">α-helices and β-strands. However, when the protein has only one prominent type of structural elements, it failed to recognize the structural elements correctly and did mis-labelling of the secondary structural elements for e.g In the attached pic, the protein which I used for labelling purpose has all α-helices but the script has mis-labelled them as all β-strands. Please have a look into this issue.</span><o:p class=""><span style="font-family: Calibri, Helvetica, sans-serif;" class=""> </span></o:p></p><p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.693333625793457px; font-size: 11pt; font-family: Calibri, sans-serif; text-align: justify;"><span style="background-color: white; font-family: Calibri, Helvetica, sans-serif;" class=""><br class=""></span></p><p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.693333625793457px; font-size: 11pt; font-family: Calibri, sans-serif; text-align: justify;"><span style="background-color: white; font-family: Calibri, Helvetica, sans-serif;" class="">Thanks a lot!</span><span style="background-color: white;" class=""><o:p class=""><span style="font-family: Calibri, Helvetica, sans-serif;" class=""> </span></o:p></span></p><p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.693333625793457px; font-size: 11pt; font-family: Calibri, sans-serif; text-align: justify;"><span style="background-color: white; font-family: Calibri, Helvetica, sans-serif;" class="">Arun</span><span style="background-color: white;" class=""><o:p class=""><span style="font-family: Calibri, Helvetica, sans-serif;" class=""> </span></o:p></span></p></div><div 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;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;" class="">Arun Gupta PhD, MRSC</span></div><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><div style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><span style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;" class="">Research Fellow</span></div><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><div style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><span style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;" class="">Challis & Lewandowski Group</span></div><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><div style="margin: 0px; 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font-size: 10pt;" class="">United Kingdom</span></span></div></div></div></div></div><div id="appendonsend" 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;" class=""></div><hr tabindex="-1" 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; display: inline-block; width: 520.375px;" class=""><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; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" 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;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, November 8, 2021 10:28 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Gupta, Arun <<a href="mailto:Arun.Gupta@warwick.ac.uk" class="">Arun.Gupta@warwick.ac.uk</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] Labelling w.r.t Secondary structure elements</font><div class=""> </div></div><div class="" 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; word-wrap: break-word; line-break: after-white-space;">Hi Arun,<div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Glad it's useful to you. For the benefit of others, I have put a slightly improved version of the script on the <a href="https://rbvi.github.io/chimerax-recipes/" class="">ChimeraX Recipes</a> site. The improvement is that it will prefix the labels with the chain ID if there is more than one chain in the structure.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Nov 4, 2021, at 2:10 AM, Gupta, Arun <<a href="mailto:Arun.Gupta@warwick.ac.uk" class="">Arun.Gupta@warwick.ac.uk</a>> wrote:</div><br class="x_Apple-interchange-newline"><div class=""><div class="" style="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; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Thanks a lot Eric. Script works pretty nicely. It saves a lot of time.</div><div class="" style="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; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="" style="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; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Best wishes,<div class="">Arun</div></div><div class="" style="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; text-decoration: none;"><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div id="x_Signature" class=""><div class=""><div id="x_divtagdefaultwrapper" dir="ltr" class="" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;"><div class="" style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;"><span class="" style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;">Arun Gupta PhD, MRSC</span></div><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><div class="" style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;"><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><span class="" style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;">Research Fellow</span></div><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><div class="" style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;"><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><span class="" style="font-family: Calibri, Helvetica, sans-serif; color: rgb(56, 56, 56); font-size: 10pt;">Challis & Lewandowski Group</span></div><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><div class="" style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;"><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><span class="" style="color: rgb(56, 56, 56); font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;">Chemistry Department</span></div><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><div class="" style="margin: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;"><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;"></span><span class="" style="font-family: "Helvetica Neue"; color: rgb(56, 56, 56);"><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;">University of Warwick</span><br class=""><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;">Gibbet Hill Road</span><br class=""><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;">Coventry CV4 7AL</span><br class=""><span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;">United Kingdom</span></span></div></div></div></div></div><div id="x_appendonsend" class="" style="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; text-decoration: none;"></div><hr tabindex="-1" class="" style="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; text-decoration: none; display: inline-block; width: 520.375px;"><span class="" style="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; text-decoration: none; float: none; display: inline !important;"></span><div id="x_divRplyFwdMsg" dir="ltr" class="" style="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; text-decoration: none;"><font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, November 4, 2021 12:11 AM<br class=""><b class="">To:</b><span class="x_Apple-converted-space"> </span>Gupta, Arun <<a href="mailto:Arun.Gupta@warwick.ac.uk" class="">Arun.Gupta@warwick.ac.uk</a>><br class=""><b class="">Cc:</b><span class="x_Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] Labelling w.r.t Secondary structure elements</font><div class=""> </div></div><div class="" style="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; text-decoration: none;"><div class="" style="word-wrap: break-word; line-break: after-white-space;">Hi Arun,<div class=""><span class="x_x_x_Apple-tab-span" style="white-space: pre;"></span>Elaine is correct that there is no easy command equivalent for this. I wrote a short Python script to label the middle label of each secondary structure element with α/β<i class="">N</i><span class="" style="font-style: normal;"> for helices/strands respectively. Run the script simply by opening it with the open command. You can adjust the initial height of the labels by editing the first line of the script, or afterward with the "label height<span class="x_Apple-converted-space"> </span></span><i class="">N</i><span class="" style="font-style: normal;">" command. Keep in mind that secondary structure element numbering resets with each chain, so if you have a multi-chain structure then this script may not produce what you want.</span></div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="x_x_x_Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div><div class=""><span class="x_x_x_Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div></div><div class=""></div></div><div class="" style="word-wrap: break-word; line-break: after-white-space;"><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Nov 3, 2021, at 1:55 PM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="x_x_x_Apple-interchange-newline"><div class=""><div class="">Hi Arun,<br class="">Not completely sure this is what you're asking, but I'm guessing something like how "label" shows residue labels, but instead showing a label like alpha1 or beta1 for each secondary structure element (SSE)? There is nothing like that, sorry. <br class=""><br class="">Personally I would use 2D Labels before Powerpoint, but you undoubtedly have more Powerpoint skills than I do. You can enter the text, colors, arrows, etc. in 2dlabels commands, and then drag them to the desired locations with the "move label" mouse mode.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html</a>><br class=""><br class="">The closest "automatic" thing I can think of is the following, but it doesn't look good enough for a figure, partly because every residue has a label. I can't think of a simple way to only add one label per SSE. Example:<br class=""><br class="">open 2gbp<br class="">label (helix | strand) attribute ss_id height 1.2<br class=""><br class="">... that just gives an integer 1 for residues in first strand and first helix, 2 for second strand and second helix, and it doesn't say whether it's a strand or helix (0 for all coil). You could also label by secondary structure type, but that attribute is also an integer, not the words or greek letters alpha and beta (ss_type 1 for helix, 2 for strand).<br class=""><br class="">label delete<br class="">label (helix | strand) text "{0.ss_type}:{0.ss_id}" height 1<br class=""><br class="">see "label" options<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options</a>><br class="">and attribute names<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html</a>><br class=""><br class="">Again, I'd use 2dlabels, but to assist with identifying which SSE is which, I might use the first label command example above (and delete those labels when I was done), or just rainbow the chain and go progressively from blue to red.<br class=""><br class="">I hope this helps,<br class="">Elaine<br 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=""><blockquote type="cite" class="">On Nov 3, 2021, at 1:10 PM, Gupta, Arun via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello, <br class="">I was wondering is there a quick fix way around by which we can define in an automated fashion the numbering and further labelling of secondary structural elements labels, alongside the structure, based on “dssp” described symbol notation "for example starting from α1/β1-α10/β14 " for any protein instead of manually labelling later in Power point. <br class="">Thanks a lot! <br class="">Arun <br class=""></blockquote><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></div></blockquote></div></div></div></div></div></blockquote></div><br class=""></div></div><span id="cid:FAA9B944-B3C3-41DC-AD4F-749B9020C0F2"><091121__Structure_1.png></span></div></blockquote></div><br class=""></div></body></html>