[chimerax-users] Color by RMSD for nucleic acid

[Rundlet, Emily]

Thank you so much, Elaine and Eric.

The "sequence header rmsd setting atoms backbone" command worked perfectly!
________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Monday, May 2, 2022 5:53 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>; Rundlet, Emily <Emily.Rundlet at STJUDE.ORG>
Subject: Re: [chimerax-users] Color by RMSD for nucleic acid

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Hi Emily,
        As Elaine says, that is a bug.  Looking at the code, I can see there is a workaround you can use until the bug is fixed.  Use the command "sequence header rmsd setting atoms backbone" which will switch from using carbon alphas to the backbone atoms appropriate for the polymer type of the chain.  You should then see actual histogram values in the RMSD header on the sequence and the "color byattribute seq_rmsd" command should work.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab


> On May 1, 2022, at 9:02 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Emily,
> That is a bug -- the problem is that currently, ChimeraX assumes the alignment is protein and tries to calculate the alpha-carbon RMSD rather than using nucleic-acid atoms.  I will create a bug ticket with you as the reporter so that you will be notified of any fixes.
>
> Thanks for reporting it!
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Apr 30, 2022, at 10:59 AM, Rundlet, Emily via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hi ChimeraX developers,
>>
>> Is there a way to color nucleic acids by seq_rmsd?
>>
>> When I use the following, no atoms are colored.
>>
>> mm #1 to #2 matrix Nucleic showAlignment true
>> color byattribute seq_rmsd  #2
>>
>> Thank you in advance for your help!
>>
>> -Emily
>>
>
>
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