[Chimera-users] square of density volume

Tom Goddard goddard at cgl.ucsf.edu
Wed Apr 14 00:11:07 PDT 2010

Hi Ryo,

  If you just want to average two maps with a certain weighting use the 
"vop add" command with the scaleFactors argument.  For example,

    vop #1,2 scaleFactors 0.75,0.25

gives a 3:1 weighting of maps 1 and 2.  Here is documentation:


The morphing can work too.  The poor quality display is probably just 
the volume viewer dialog step size being set to 2 instead of 1, so the 
full resolution data is not being shown.


> Hi Tom, chimera staffs, and users,
> I have a question about the vop morph tool.
> I want to average two volumes of the electron density map at the 
> different rate (for example, 1:1, 2:1, 3:1, ...).
> I found the vop morph tool which can make an intermediate volume 
> between two structures.
> So, I used the vop morph tool to average two volumes.  For example, to 
> obtain the 1:1 averaging map of two density maps, the step size was 
> set at 0.5 and I got a fraction of 0.5 as a 1:1 averaging map.
> However, the resolution of the resulting map clearly dropped and the 
> map seemed to be vague.
> Does some (filtering? smoothing?) effect was included in the vop morph 
> tool to decrease the resolution (because the vop morph tool should be 
> made to make a smooth varying movie between two structures)?
> If so, is there some other chimera tool to simply average two (or 
> more) volumes of the density map at the rate of 1:1 (or favorably 2:1, 
> 3:1,...)?
> Sincerely,
> Ryo

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