[Chimera-users] RMSD fit of an object to atom

Navnit Kumar Mishra navnit at chemi.muni.cz
Thu Mar 8 07:47:03 PST 2007

Hello Tom and Eric;

I really appreciate your help and suggestion. I would be glade to 
receive the script.

Concerning density peak selection, Tom could you tell me how can I add 
shortcut key to move atom to local density maxima.

Thanking you,

Eric Pettersen wrote:

> On Mar 7, 2007, at 12:13 PM, Tom Goddard wrote:
>>  I didn't understand your explanation of why 4 points are needed for 
>> an alignment with the match command.  It looks like only 3 are needed 
>> for a unique match.  In your example with points ABC and DEF you 
>> suggested that the match could either pair A with D, B with E, and C 
>> with F or it could pair A with F, B with E, C with D.  But the match 
>> command specifies the desired pairing so only one of those is 
>> possible for any match command invocation.
> Tom's right in that with the correspondences specified, 3 points is 
> enough for a unique superposition.  After some investigation, it turns 
> out that back in MidasPlus we used a different superposition algorithm 
> and that algorithm required at least four points to work.  Chimera 
> uses a different algorithm -- and there is no minimum!  It will work 
> with one point.  So the 4-point minimum is an unnecessary restriction 
> and will be removed in future releases (though it will warn about 
> non-uniqueness if you use less than 3 points).
> Navnit, I can send you a file with the restriction removed if you 
> want.  Let me know.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>
>                         http://www.cgl.ucsf.edu

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