<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Steven,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Uninstalling SEQCROW should allow you to use the regular rmsd command. I will update SEQCROW to change the name of the rmsdAlign command to avoid this type of conflict, though the update will not be compatible with ChimeraX 1.1.1. There were significant changes
between ChimeraX 1.1 and 1.2, so I'd have to go back pretty far to get things to work with 1.1-era ChimeraX.<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
You can uninstall SEQCROW by running "toolshed uninstall SEQCROW"</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Tony<br>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Steven Truong via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, October 12, 2021 7:18 PM<br>
<b>To:</b> ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Use values printed from Log inside a script (e.g. RMSD)</font>
<div> </div>
</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br>
<br>
<div>Hi Tony and Elaine,
<div class=""><br class="">
</div>
<div class="">I am currently using ChimeraX-1.1.1. I think I may have found the issue then. Whenever I type “rmsd” in the command line, it defaults to rmsdAlign. Is there a way to fix this? I’m not sure if it’s a bug or something I did on my end. </div>
<div class=""><br class="">
</div>
<div class="">You can see this in the screenshot below (I typed rmsd and get rmsdAlign in the log).</div>
<div class=""><br class="">
</div>
<div class=""><img id="x_5C48F7A6-731A-4D6F-BEE0-996EC31957F9" width="937" height="255" class="" data-outlook-trace="F:1|T:1" src="cid:67EE263D-997E-490B-9A0B-2178D2833EFE"></div>
<div class=""><br class="">
</div>
<div class="">Thank you for the help,</div>
<div class="">Steven</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 12, 2021, at 11:48 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="">Hi Steven,<br class="">
Are you using a super-ancient version of ChimeraX? I'm not aware if there was ever an rmsdAlign command. By command I mean what you would type into the actual command line or use in a command file. Maybe there is some other way to access the functionality
via python.<br class="">
<br class="">
However, if the structures are not already superimposed, you may want to use the "align" command instead of the "rmsd" command ... the former calculates a best-fit RMSD whereas the latter just calculates RMSD in the current positions without trying to superimpose/fit
them, so if the structures are in some random positions relative to each other you will get a huge value.<br class="">
<br class="">
align<br class="">
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html</a>><br class="">
<br class="">
rmsd<br class="">
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html</a>><br class="">
<br class="">
Best,<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 Oct 12, 2021, at 2:39 PM, Steven Truong via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Hi Eric, Tony, et al.,<br class="">
<br class="">
Thank you for answering my question. For now, I’ll be doing what Tony suggested re: assigning a value with the RMSD command. Currently, I’m having issues with using “rmsd” by itself (it seems like rmsdAlign is the only valid command). I’m assuming this is
the same command, just named differently.<br class="">
<br class="">
Re: your inquiry, the protein does have the same sequences. However, the chain ID is critical, since I am attempting to “stitch” fragments of proteins at different residues. For example, if I align a fragment to the wrong chain, it will have a bond hanging
on the other side of the protein (not good!). This stitching can be done manually (e.g. if it’s not the right chain or residue ID, I can simply move the fragment), but I am trying to automate this process via Python scripts. Additionally, I have been doing
the bond-forming on Chimera (with the command “bond”). I’m not sure if there’s a better way of going about this, but my idea currently is to 1. Identify which chains match up, 2. Align fragments from 1 protein to the other (which may have different chain
ID identifiers), 3. Make bonds on Chimera.<br class="">
<br class="">
Many thanks,<br class="">
Steven <br class="">
<br class="">
<blockquote type="cite" class="">On Oct 12, 2021, at 9:31 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Hi Steven,<br class="">
<br class="">
<blockquote type="cite" class="">On Oct 12, 2021, at 12:39 PM, Steven Truong via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Dear ChimeraX Admins,<br class="">
<br class="">
I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script.
<br class="">
<br class="">
Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X.
<br class="">
</blockquote>
<br class="">
Tony answered this.<br class="">
<br class="">
<blockquote type="cite" class="">Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better
idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains?<br class="">
</blockquote>
<br class="">
Do these chains have the same sequence? Also, I'm a little uncertain what "map one chain to the other" means exactly. At any rate, the matchmaker command can be used to superimpose one chain onto another and report the backbone (CA or C4'/P) RMSD for the
match. By default matchmaker iterates its match, pruning off poorly matching regions and re-matching to get a good fitting "core" match, and will report RMSD values for both the core region and across the entire sequence. You can turn off the iteration if
desired with matchmaker's "cutoffDistance none" option.<br class="">
<br class="">
--Eric<br class="">
<br class="">
Eric Pettersen<br class="">
UCSF Computer Graphics Lab<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
Thank you,<br class="">
Steven Truong<br class="">
Cambridge University<br class="">
</blockquote>
</blockquote>
</blockquote>
<br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</body>
</html>