[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.
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 Pettersen
> UCSF Computer Graphics Lab
> pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>
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