[Chimera-users] Coot capabilities in Chimera

Tom Goddard goddard at sonic.net
Thu Jan 22 16:55:56 PST 2015


Hi Mario,

  This is a good question and many researchers pursuing 3-4A cryoEM structures are asking me the same question.  I developed the Chimera map capabilities, much of it done 5 or more years ago when a 10A map was a good resolution.  As the maps started coming out with resolutions seen for large molecules using x-ray crystallography I thought it would be natural to use x-ray refinement tools on those.  I still think that is sensible advise.  But it is apparent that refining an x-ray map at 3-4 Angstroms resolution was never easy and is not easy now.  Chimera does not have tools to let you 
refine structures at the residue level.  My observation is that most people working on such maps use multiple visualization, analysis and refinement programs including Chimera because no one program can do everything.  Since I don’t know Coot well I can’t comment on what aspects of the work Chimera would do better.

  I have long discussed with Matt Baker in Wah Chiu’s lab integrating his Gorgon high resolution structure refinement for cryoEM into Chimera.  It is something we are interested in for our next generation Chimera 2 that we have been working on for a year.  We are still working on more basic capabilities of Chimera 2 so I can’t say that high resolution map capabilities will be available in Chimera soon.

  I think others who are refining 3-4 A cryoEM maps will have the best advice on which of the many software options has worked for them.

	Tom


> On Jan 21, 2015, at 2:14 PM, Mario J. Borgnia wrote:
> 
> Dear all,
> 
> WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves
> refining structures. The blunt question is, should I move to Coot and
> leave behind Chimera for that or are there overlapping functions and
> what will I be missing if I choose to stay with Chimera.
> I have some ideas about the answers but would like to read what the
> developers and power users have to say on the issue.
> 
> Thanks!!!
> 
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