[Chimera-users] Make volume have mean 0, standard deviation 1

[Thomas Goddard]

Hi Terry,

   Chimera does not automatically scale density maps.  You can use a 
command like

	vop scale #0 shift -8.0 factor 0.2

to shift map #0 values by -8.0 and then scale by 0.2.  If the mean were 
8.0 and standard deviation were 5.0 then this would normalize to mean 0 
and SD 1.0.  This creates a new volume data set.  There is no capability 
to shift and scale an existing map without making a new volume data set. 
   The Volume Filter dialog (menu Tools / Volume Data) can do the same 
thing. Python code to do the shift/scale is in

	chimera/share/VolumeFilter/scale.py

There is a menu entry Tools / Volume Data / Volume mean, SD, RMS that 
reports the mean and SD and RMS about zero of the highlighted map in the 
volume dialog.  There is no command equivalent (I should make the 
measure command do this).  The Python code that does this is in

	chimera/share/VolumeStatistics/__init__.py

   Tom


-------- Original Message --------
Subject: question about ccp4 formatted map density
From: Terry Lang
To: Tom Goddard
Date: 11/23/09 11:39 AM

> Hey Tom,
> 
>       I am looking into some new schemes for scaling electron map 
> density.  I know you said that the scaling to a mean of zero and 
> standard deviation of 1.0 is implemented in the current release.  
> However, I can't seem to find where the code is located.  I am really 
> interested in figuring out where exactly scaling happens and if it's 
> automatic or needs to be requested.  Any input you can provide would be 
> greatly appreciated!
> 
> Sincerely,
> Terry
>