[Chimera-users] Fit MAP to MODEL

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 17 14:51:01 PDT 2009

Hi Michael,
Saving a rotated map requires resampling it at new grid positions  
because none of the map formats include an option for specifying a  
rotation in the header.  However, with resampling there is some loss  
of resolution because interpolation is required to get the values at  
the new grid point locations.  That is why we normally recommend  
saving the rotated PDB instead when the goal is to have a PDB and map  
that fit together.

However, if you are going to average maps they may need to be  
resampled onto a consistent grid anyway.  Resampling a map onto the  
grid of another map can be done with "vop resample" as described here:


For example,
vop resample #0 onGrid #1 [other-options]

You would want to figure out which map's grid you want to do the final  
averaging on and use the fewest resamplings as possible to achieve  
that, for minimal loss of data quality.  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 Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:

> HI-
> We are using chimera to fit xxx model into rho map. I'd like to fit  
> rho map
> into xxx model. That is, rotate and translate my map to coincide  
> with a
> fixed orientation of the model. Of course, then I can average rho1,  
> rho2
> etc. We can get around the "map" part of the "fit (button1) to map
> (button2)" by running pdb2mrc to turn xxx model into xxx map. No  
> problem.
> But how do we write out the new rotated version of the rho map when  
> we are
> done fitting? Thanks.

More information about the Chimera-users mailing list