[Chimera-users] EM density fitting

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 28 09:20:00 PST 2011

Hi Hao,
All the tools in Chimera that do the fitting also report the fitting score.   First open your map file and the PDB file(s) in Chimera, then perform some fitting.  There are several ways, which I will try to summarize here:

For fitting one PDB structure at a time into the map:

(A) The Fit in Map tool (under Tools... Volume) locally optimizes the fit and reports fitting score.  

This tool does not do global searching, so you would first need to put the structure in the map in a reasonable location yourself, by "freezing" one and moving the other as described here:


(B) the "fitmap" command can do global searching with one PDB structure:
there is also a video tutorial about that:

Fitting scores from the command are reported in the Reply Log (in menu under Favorites).

However, it sounds like you might have multiple PDB structures that are all supposed to fit into one map.  In that case, fitting one structure at a time may not be what you want, since the best positions of the individual structures might overlap with each other.  So,  for fitting multiple PDB structures into a map:

(C) the "fitmap" command can do sequential fitting of multiple PDB structures:
... but currently, this cannot be combined with global search.  So you would have to first place the structures in reasonable positions yourself, as mentioned above in (A).

(D) the MultiFit tool (under Tools... Volume) will use a web service to place multiple PDB structures into a map.  This is a longer calculation if you want to do a global search (you would have to turn on the "Fit globally" checkboxes to do that):

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 26, 2011, at 6:37 PM, dhacademic wrote:

> Hi,
> I have an EM density map of a protein, as well as several PDB structures, and want to find the most possible structure with the lowest fitting score. Can anyone tell me know how to calculate the fitting score between the EM-density map and a PDB structure in chimera? Many thanks!
> Best,
> Hao

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