[chimerax-users] RMSD command in ChimeraX

[Hrvoje Rimac]

Dear Elaine,

thank you for the answer. I guess the best solution is either to
explicitly list the order of atoms in Chimera (not ChimeraX) or change the
order in the pdb files. In this way I get what I want. I guess writing a
script for that is inevitable :D

P.S. I see a ticket has been raised for the rmsd equivalent in ChimeraX.
Looking forward to a permanent solution.


Thank you again,
Hrvoje


> 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> 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>
>>
>> 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> 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/