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

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 25 11:07:23 PDT 2011

Hi John,
	I've now changed the code so that MatchMaker doesn't try to compute  
assignments for CA-only structures but instead uses existing  
assignments (if any).  That change will be in the next 1.6 daily build.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Aug 25, 2011, at 9:40 AM, Elaine Meng wrote:

> 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
> ----------
> 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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> Chimera-users at cgl.ucsf.edu
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