[Chimera-users] MatchMaker in version 1.5.3 (build 33475)

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 25 09:40:28 PDT 2011

Hi John,
You're right, this behavior is because 1HPB is a CA-only structure, i.e. it contains only the alpha-carbon of each residue.

The reason it changes from normal-looking ribbons to licorice is that by default, MatchMaker recomputes the secondary structure assignments of the structures.  We found that approach to generally improve the superpositions because the pre-existing assignments of different structures were often inconsistent with one another.  Since 1HPB only has CA atoms, no secondary structure is found and the whole thing is now shown in the "turn" representation, which looks like licorice.

Actually I'm surprised it looks as good as it does when first opened, since one might think there wouldn't be enough information to orient the ribbons even though the strand and helix assignments are included in the PDB header information.

You can turn off the MatchMaker option "Compute secondary structure assignments" to prevent 1HPB or other CA-only structures from losing their original secondary structure assignments, if any, and turning into licorice.

I hope this helps!   Glad to hear you are using Chimera in your classes, and happy to help if you run into other issues.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 25, 2011, at 8:54 AM, John Rose wrote:

> Hi,
> I have been using chimera since the late 1990s.  In the previous versions I could use MatchMaker to superimpose two molecules and all the atoms were moved with the model.  Noe I find that when I use MatchMaker the models are aligned BUT the non-reference structures shoe up in a  licorice stick representatuin and I have not been able to either (1) generate a ribbon drawing of the non-reference structures or (2) get an all atom view of the non-reference structures.  Am I missing something?  The two structures are 1wdn and 1hpb.  
> This happens on both the MAC and Linux platforms.
> This feature is important to several classes I teach so any help you can give me would be greatly appreciated.
> John

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