[Chimera-users] UCSF Chimera License Inquiry

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 16 14:52:13 PDT 2019

Dear Ella Morishita,
In general, Chimera Matchmaker can be used to superimpose nucleic acid structures of similar sequence and 3D structure, but it is impossible to guarantee or know ahead of time whether it would work well on a specific pair of structures.

However, Chimera also includes other methods of superimposing structures.  There is a “match” command that does a least-squares fit of the specified atoms.  You just have to give the same number of atoms from each structure in the command, which is more work than just using Matchmaker (which figures out the atom pairing for you by aligning the biopolymer sequences).  If there is very little sequence similarity and/or 3D structure similarity, Matchmaker is less likely to work.  The various methods of superposition in Chimera are outlined here:


Here is a brief example and image of result of using Matchmaker on two tRNA structures, where I delete all chains except A in each, and superimpose with matchmaker command.  I didn’t try to shop around for tRNAs that would work well, just searched for tRNA and RNA-only structures at the RCSB PDB and these were the first two I tried, but I might have been lucky.  Commands:

open 4mgm
open 3rg5
delete ~ :.a
mm #0 #1 show true matrix Nucleic

Although above the alignment it says “RMSD: ca” it should be “RMSD: C4’” because these are nucleic acids rather than proteins.

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

P.S. we have the same initials  :-)

> On Apr 15, 2019, at 2:14 PM, Williams, Joanne <Joanne.Williams at ucsf.edu> wrote:
> Hello User Help Team,
> Can you help address Ella’s question below regarding using Chimera with Matchmaker? I let her know that there are no trial versions of Chimera. 
> Thank you,
> JoAnne
> From: Ella Czarina Morishita <ecm at vi14si.com>
> Date: Friday, April 12, 2019 at 6:48 AM
> To: "chimera at cgl.ucsf.edu" <chimera at cgl.ucsf.edu>
> Subject: UCSF Chimera License Inquiry
> Dear Sir/Madam, 
> My name is Ella Morishita, and I am a principal investigator at a biotech in Japan. I  am interested in downloading Chimera, but I was not sure if we are supposed to pay for the license for the use of Chimera at our biotech. I am currently running a case study involving structures of nucleic acids and would like to superimpose the structures using Chimera and Matchmaker. I am also not sure if Chimera and Matchmaker would work, so I was wondering if there is any trial package we can avail?
> Thank you.
> Best regards, 
> Ella Morishita
> ********************************************
> Principal Investigator
> Veritas In Silico Inc.
> 1-11-1 Nishi-Gotanda, Shinagawa-ku, Tokyo 141-0031
> Tel: 03-6421-7537 Fax: 03-6421-7538
> Email: ecm at vi14si.com
> ********************************************

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