[Chimera-users] Fit in map equivalent for surfaces?

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 28 09:20:17 PST 2016

Hi Joe,
As you saw, “Fit in Map” performs local optimization.  However, additional options are available in the “fitmap” command, including a global search with random initial placement to give diverse starting points for local optimization.  I’d try that out before doing anything fancier.

Fit in Map GUI:

fitmap command:
… global search options:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 28, 2016, at 4:50 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> Thanks Elaine, that has done the job.
> Out of curiosity, I noticed from your documentation that the fitting actually only 'kicks in' after the densities are overlaid by hand roughly first. Is there any mechanism for the objects to move to one another as in the MatchMaker function (considering automating this process)?
> Alternatively, I could envisage perhaps centroiding both densities, and moving the centroids to occupy the same space, as which point fitting would take over. Any thoughts?
> Joe Healey

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