[Chimera-users] coloring 3D maps according to local cross-correlation fit of docked PDB structures

[Tom Goddard]

Hi J-F,

   I added the "vop localCorrelation" command to Chimera that computes 
the correlation between two maps over a moving window of size N by N by 
N voxels.  The result can be used to color surfaces or atoms as shown in 
the attached picture of a zinc transporter (3j1z) and 13 Angstrom 
resolution EM map (EMDB 5450).  To color the surface I used

     open 3j1z
     molmap #0 13
     open emdbID:5450
     vop localCorrelation #0 #1 windowSize 5 model #2
     scolor #1 volume #2 cmap .8,blue:0.9,white:1,red
     transparency 30 #1

If you leave off the windowSize option to vop localCorr it defaults to 5 
voxels.  The colored atoms in the picture and the color key were made 
with the Values at Atom Positions dialog (menu Tools / Volume Data / 
Values at Atom Positions) and the Render by Attribute dialog (menu Tools 
/ Depiction / Render by Attribute).

   The calculation is quite slow because it is being done in Python. It 
took a minute for the 28 x 32 x 37 simulated map and 160 x 200 x 160 EM 
map.  It computes local correlation at the grid points of the first map 
in the vop localCorr command.  It will only be a little effort to do the 
calculation in C++ which will be one hundred times faster but I don't 
think I have time to do that today.

   The new command will be in tonight's daily build.

     Tom


-------- Original Message --------
Subject: Re: [Chimera-users] coloring 3D maps according to local 
cross-correlation fit of docked PDB structures
From: Jean-Francois Menetret
To: Tom Goddard
Date: 10/19/12 8:35 AM
> Hi Tom,
>
> we would like tocolor the surface representation of our molecule with 
> the local correlation score between the fitted atomic models and the 
> EM-maps;
> you can find an example in figureS3 of Hipp et al. Nucleic Acids 
> Research, 2012, Vol. 40, No. 7 3275--3288
>
> best wishes
> J-F
>
> On Thu, Oct 18, 2012 at 7:37 PM, Tom Goddard  wrote:
>
>     Hi J-F,
>
>      Do you mean if the correlation of a molecular model with a map is
>     0.9 then color the whole map blue?  Or do you want to color just
>     the region of the map near the molecule blue.  Or do you wan the
>     map be colored in different colors, each representing the local
>     correlation of the molecule to the map near the point where that
>     color is shown?  If this last case, how would you define the
>     "local correlation"?  Probably you would want to color the
>     molecule in that case not the map since it would give a better
>     view of the whole volume rather than just its envelope.
>
>         Tom
>
>
>
>     -------- Original Message --------
>     Subject: [Chimera-users] coloring 3D maps according to local
>     cross-correlation fit of docked PDB structures
>     From: Jean-Francois Menetret
>     To: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
>     Date: 10/18/12 6:24 AM
>>     Dear users,
>>     we would like to color aCryo-EM map according to the
>>     cross-correlation fit of docked PDB structures.
>>     Is that possible in Chimera ?
>>     Best wishes
>>     J-F Menetret
>
>


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