[Chimera-users] map normalization; ccp4 file saving

Tom Goddard goddard at cgl.ucsf.edu
Mon Jul 26 13:58:44 PDT 2010

Hi Jean Paul,

   Yes, you would use the "vop scale" command to scale a map so it has 
the same normalization as another map, for example,

     vop scale #1 factor 0.5721

You could choose the scale factor to produce the same root-mean-square 
map value (RMS).  Menu entry Tools / Volume Data / Volume Mean, SD, RMS 
will report the RMS value for the highlighted map in the volume dialog.  
You would use the ratio of the RMS values for the two maps as the scale 
factor.  You might also want to make the maps have the same mean and 
this can be done with the "shift" keyword to "vop scale".  Lastly be 
careful your map is saved as integer values and you scale it down to the 
range 0 - 1 you'll get a bad result.  The "type" keyword to "vop scale" 
let's you convert to floating point data representation:

     vop scale #1 factor 0.5721 shift 0.034 type float32

Here's the "vop scale" documentation:


   Chimera only writes MRC2000 format maps.  This differs so minutely 
from CCP4 format that I am surprised that COOT will not read a Chimera 
MRC2000 map.  I'll have to install COOT and figure out what it is about 
the Chimera MRC files it doesn't like.


> hello,
> i would like to pose two questions:
> 1. is there a way of adjusting one map so that it's adjusting to the 
> levels of another map?
> i believe it should be achievable with "vop" command, but i am not 
> sure whether the
> vop scale is the appropriate thing to use.
> 2. would it be possible to save the output map as a ccp4 map? 
> currently you're permitting
> mrc saving, which is not that very much different from ccp4, so i was 
> wondering if it was
> possible to add this feature. the difference is large enough so that 
> coot does not allow for
> map loading of mrc files.
> best regards,
> jean-paul

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