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

[Tom Goddard]

Hi J-F,

I replace the Python local correlation calculation with C++ so it is 
relatively fast now -- tens seconds using two 256 by 256 by 256 maps 
with window size 5 pixels.

     Tom

> 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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