[chimerax-users] RMSD command in ChimeraX

Fri Jun 19 12:17:28 PDT 2020

Thank you Anthony,

in Chimera after sorting the atoms (and PyMOL) I also got 0.465. The value
of 0.454 I got when I calculated it by hand in Excel, it could be a
rounding issue (even though it is a little big for that) or I could've
made a mistake somewhere, but I don't see where since the value of 4.147
is identical for both Excel and Chimera. In either case, thank you.

Best regards,
Hrvoje

I will definitely try it.
> Hi Tony,
> 	Itâ€™s possibly because of the atom ordering?  By default, the atoms
> returned by an AtomsArg arenâ€™t sorted, since sorting is an expensive
> operation if the number of atoms is large (e.g. youâ€™re coloring a
> ribosome).  To get the atoms for your rmsdAlign command to be sorted, use
> an OrderedAtomsArg instead.
>
> â€”Eric
>
>> On Jun 19, 2020, at 11:54 AM, Anthony James Schaefer
>> <tony.schaefer at uga.edu> wrote:
>>
>> Dr. Rimac,
>>
>> 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.
>>
>> Here's my bundle's GitHub:https://github.com/QChASM/SEQCROW/tree/dev
>> <https://github.com/QChASM/SEQCROW/tree/dev>
>>
>> The installation instructions can be found in the README lower on that
>> GitHub page.
>>
>> 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.
>>
>> Best,
>>
>> Tony
>>
>> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu
>> <mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Elaine Meng
>> <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
>> Sent: Friday, June 19, 2020 10:56 AM
>> To: Hrvoje Rimac <hrimac at pharma.hr <mailto:hrimac at pharma.hr>>
>> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu
>> <mailto:chimerax-users at cgl.ucsf.edu>>
>> Subject: Re: [chimerax-users] RMSD command in ChimeraX
>>
>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>
>>
>> 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.
>> Best,
>> Elaine
>>
>> > On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng at cgl.ucsf.edu
>> <mailto:meng at cgl.ucsf.edu>> wrote:
>> >
>> > Dear Hrvoje Rimac,
>> > 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.
>> >
>> > 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.
>> >
>> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>>
>> >
>> > 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.
>> >
>> > I opened your two files, then command:
>> >
>> > align #1 toAtoms #2 move nothing
>> > RMSD between 24 atom pairs is 0.252 angstroms
>> >
>> > Also tried "matchAtomNames" option:
>> >
>> > align #1 toAtoms #2 matchAtomNames true move nothing
>> > RMSD between 24 atom pairs is 0.252 angstroms
>> >
>> > Even if I list all the atoms, I still get the same value.
>> >
>> > align
>> #1 at 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 at 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
>> > RMSD between 24 atom pairs is 0.252 angstroms
>> >
>> > I hope this helps,
>> > Elaine
>> > -----
>> > Elaine C. Meng, Ph.D.
>> > UCSF Chimera(X) team
>> > Department of Pharmaceutical Chemistry
>> > University of California, San Francisco
>> >
>> >
>> >> On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac at pharma.hr
>> <mailto:hrimac at pharma.hr>> wrote:
>> >>
>> >> Hi,
>> >> I was wondering if there is a command in ChimeraX which calculates
>> RMSD
>> >> without first aligning the ligands (analog to Chimera command
>> "rmsd"). The
>> >> problem is that the order of atoms in the two pdb files is not
>> identical,
>> >> and in Chimera (1.14) the "rmsd" command (as well as the "match"
>> command)
>> >> compares the first atom to the first atom, the second to the second
>> etc,
>> >> regardless of their type (I checked this manually), so the calculated
>> RMSD
>> >> is very high. In ChimeraX this mismatching problem is resolved,
>> however
>> >> the only command I found was the "align" command which calculates
>> RMSD
>> >> after aligning the molecules (as "match" match does in Chimera). Is
>> there
>> >> a command that would calculate RMSD without aligning the molecules?
>> This
>> >> wouldn't be a problem if I had 2 ligands to compare, but since I have
>> more
>> >> than 900, it would be very time consuming to check and correct order
>> of
>> >> all atoms.
>> >>
>> >> P.S. I have attached the structures of the two ligands. The RMSD
>> values
>> >> I'm getting are:
>> >> Chimera "match": 4.064
>> >> Chimera "rmsd": 4.147
>> >> ChimeraX "align": 0.252
>> >> The value I should get: 0.454
>> >>
>> >> Best regards,
>> >> Hrvoje Rimac
>> >
>> >
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Hrvoje Rimac, PhD.
Postdoctoral Fellow
Department of Medicinal Chemistry
Faculty of Pharmacy and Biochemistry
University of Zagreb
A.Kovačića 1, 10000 Zagreb
Croatia
http://www.pharma.unizg.hr/