[Chimera-users] problem with match function (superposition)

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 14 09:23:49 PST 2011

Hi Ken,
The match command does least-squares fitting of specific atoms, the first set from one model and the second set from a second model.  "match #0 #1" wouldn't work unless model #0 and model #1 contain exactly the same number of atoms, which is usually not the case.  For example, 1cho contains water molecules and your model complex may not.  Also, that error message makes me think that maybe your complex is actually two models, e.g. #1.1 and #1.2, so that #1 would fail to specify a single model.  You can see if that is the case by looking in the Model Panel (Favorites... Model Panel in the menu).  If so, you would need to combine them into a single model, which can be done with the "copy/combine" function in the Model Panel.

After making sure your two complexes are each a single model, then instead of the match command, you would probably want to use MatchMaker (Tools... Structure Comparison... MatchMaker in the menu).  This will align the sequences of chains and figure out the pairing for you, whereas if you were using match, you'd have to figure it out yourself and enter specific residue numbers in the command.  MatchMaker uses only CA atoms to superimpose proteins and calculate RMSDs.  Take a look at the chain pairing options in that dialog.  The default is to find the best pair of chains between the two structures and use only those for the superposition and RMSD.  If you want the superposition and RMSD for multiple chains simultaneously, you would need to use the "Specific chains in reference structure with specific chains in match structure" option.  Click the Help button to see the manual page for this tool.

There is a discussion of match vs. matchmaker and other superposition methods here:

... and examples in tutorials, such as

"superpositions and alignments"

glycoside hydrolases, see "matching" section

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

On Dec 13, 2011, at 5:08 PM, Ken Shimo wrote:

> Hello,
> I'm working with evolutionary algorithms applied to protein-protein docking.
> I'd like to calculate de RMSD between the native complex and the complex achieved with my docking model. For that I was trying to make the superposition of the complexes using the match function through the Chimera command line.
> I called the function as:
> match #0 #1
> and got the following message:
> Atoms in each selection must be in the same model
> I'd like to know what am I doing wrong, or if there is anyway other way to obtain the RMSD and the superposed complexes.
> I'm using the complex code PDB 1CHO.
> Thanks for any help,

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