[chimerax-users] RMSD command in ChimeraX

Fri Jun 19 12:00:32 PDT 2020

Hi Tony,
	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 (e.g. you’re coloring a ribosome).  To get the atoms for your rmsdAlign command to be sorted, use an OrderedAtomsArg instead.

—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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