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

Derek Harris derek.harris at aggiemail.usu.edu
Mon Jul 6 18:47:32 PDT 2020


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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