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<span style="font-family: Arial, Helvetica, sans-serif;">Eric,</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">I'm using ModelArg/ModelsArg instead of AtomsArg. I'm letting AaronTools do the sorting when `sort true` is used. I've checked, and AaronTools gets the order right (at least in this case). When `sort
false` is used, I'm just using the order the atoms appear in AtomicStructure.atoms.
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<span style="font-family: Arial, Helvetica, sans-serif;">Best,</span><br>
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<span style="font-family: Arial, Helvetica, sans-serif;">Tony</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, June 19, 2020 3:00 PM<br>
<b>To:</b> Anthony James Schaefer <tony.schaefer@uga.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] RMSD command in ChimeraX</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br>
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<div>Hi Tony,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>It’s possibly because of the atom ordering? By default, the atoms returned by an AtomsArg aren’t sorted, since sorting is an expensive operation if the number of atoms is large (<i class="">e.g.</i> you’re
coloring a ribosome). To get the atoms for your rmsdAlign command to be sorted, use an OrderedAtomsArg instead.</div>
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<div class="">—Eric<br class="">
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<div class="">On Jun 19, 2020, at 11:54 AM, Anthony James Schaefer <<a href="mailto:tony.schaefer@uga.edu" class="">tony.schaefer@uga.edu</a>> wrote:</div>
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<span class="" style="font-family:Arial,Helvetica,sans-serif">Dr. Rimac,</span></div>
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<span class="" style="font-family:Arial,Helvetica,sans-serif">My bundle has a command for that. I haven't put my bundle on ChimeraX's tool shed yet, so it won't be the easiest to install.<span class="x_Apple-converted-space"> </span></span><br class="">
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<span class="" style="font-family:Arial,Helvetica,sans-serif">Here's my bundle's GitHub:</span><a href="https://github.com/QChASM/SEQCROW/tree/dev" id="LPlnk393147" class=""><span class="" style="font-family:Arial,Helvetica,sans-serif">https://github.com/QChASM/SEQCROW/tree/dev</span></a><br class="">
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<span class="" style="font-family:Arial,Helvetica,sans-serif">The installation instructions can be found in the README lower on that GitHub page.</span></div>
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<span class="" style="font-family:Arial,Helvetica,sans-serif">The command is 'rmsdAlign'. It should work as `rmsdAlign #1 toModels #2 [#3...] align false sort true`. The RMSD's are printed to the log. I tried it on your structures and got an RMSD of 0.465 instead
of 0.454. I'm not sure why I don't get the same RMSD as you.<span class="x_Apple-converted-space"> </span></span><br class="">
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<span class="" style="font-family:Arial,Helvetica,sans-serif">Best,</span></div>
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<span class="" style="font-family:Arial,Helvetica,sans-serif">Tony</span><br class="">
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" class="">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf
of Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Friday, June 19, 2020 10:56 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Hrvoje Rimac <<a href="mailto:hrimac@pharma.hr" class="">hrimac@pharma.hr</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] RMSD command in ChimeraX</font>
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<div class="x_PlainText">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br class="">
<br class="">
<br class="">
Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that.<br class="">
Best,<br class="">
Elaine<br class="">
<br class="">
> On Jun 19, 2020, at 7:48 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
><br class="">
> Dear Hrvoje Rimac,<br class="">
> In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.<br class="">
><br class="">
> In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain
IDs, which may help.<br class="">
><br class="">
> <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html</a>><br class="">
><br class="">
> The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two
ligands.<br class="">
><br class="">
> I opened your two files, then command:<br class="">
><br class="">
> align #1 toAtoms #2 move nothing<br class="">
> RMSD between 24 atom pairs is 0.252 angstroms<br class="">
><br class="">
> Also tried "matchAtomNames" option:<br class="">
><br class="">
> align #1 toAtoms #2 matchAtomNames true move nothing<br class="">
> RMSD between 24 atom pairs is 0.252 angstroms<br class="">
><br class="">
> Even if I list all the atoms, I still get the same value.<br class="">
><br class="">
> align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing<br class="">
> RMSD between 24 atom pairs is 0.252 angstroms<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="">
><br class="">
>> On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <<a href="mailto:hrimac@pharma.hr" class="">hrimac@pharma.hr</a>> wrote:<br class="">
>><br class="">
>> Hi,<br class="">
>> I was wondering if there is a command in ChimeraX which calculates RMSD<br class="">
>> without first aligning the ligands (analog to Chimera command "rmsd"). The<br class="">
>> problem is that the order of atoms in the two pdb files is not identical,<br class="">
>> and in Chimera (1.14) the "rmsd" command (as well as the "match" command)<br class="">
>> compares the first atom to the first atom, the second to the second etc,<br class="">
>> regardless of their type (I checked this manually), so the calculated RMSD<br class="">
>> is very high. In ChimeraX this mismatching problem is resolved, however<br class="">
>> the only command I found was the "align" command which calculates RMSD<br class="">
>> after aligning the molecules (as "match" match does in Chimera). Is there<br class="">
>> a command that would calculate RMSD without aligning the molecules? This<br class="">
>> wouldn't be a problem if I had 2 ligands to compare, but since I have more<br class="">
>> than 900, it would be very time consuming to check and correct order of<br class="">
>> all atoms.<br class="">
>><br class="">
>> P.S. I have attached the structures of the two ligands. The RMSD values<br class="">
>> I'm getting are:<br class="">
>> Chimera "match": 4.064<br class="">
>> Chimera "rmsd": 4.147<br class="">
>> ChimeraX "align": 0.252<br class="">
>> The value I should get: 0.454<br class="">
>><br class="">
>> Best regards,<br class="">
>> Hrvoje Rimac<br class="">
><br class="">
><br class="">
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