[Chimera-users] Difference in alignment of cofactor between Chimera and ChimeraX

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 7 08:35:35 PDT 2020

Hello Derek,
It does not make sense for the cofactor alignment to be different if the protein alignment is the same, because the cofactors are just moved rigidly along with their proteins. Also the results should be identical between Chimera and ChimeraX, assuming you are using the same options.

I get exactly the same alignment between these two proteins in the Chimera vs. ChimeraX.

Chimera commands (including display ligand only):
open 3u7q
open 5n6y
mm #0 #1
show ligand

ChimeraX commands:
open 3u7q
open 5n6y
mm #2 to #1
show ligand

In both programs, I get the same RMSD message to the Log:

RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998)

In both programs, matchmaker ends up choosing to align chain A to chain A.  Thus the cofactors in chains A are better superimposed than the ones in the other chains.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 6, 2020, at 6:47 PM, Derek Harris <derek.harris at aggiemail.usu.edu> wrote:
> Hello,
> I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command.
> The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely.
> The two structures I am trying to align are 3U7Q and 5N6Y.
> Thanks in advance for any assistance you can offer!
> Derek Harris
> Postdoctoral Fellow
> Seefeldt Lab
> Department of Chemistry and Biochemistry
> Utah State University

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