[Chimera-users] coloring 3D maps according to local cross-correlation fit of docked PDB structures
goddard at sonic.net
Fri Oct 19 15:31:12 PDT 2012
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.
> 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.
> -------- 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
>> you can find an example in figureS3 of Hipp et al. Nucleic Acids
>> Research, 2012, Vol. 40, No. 7 3275--3288
>> best wishes
>> 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.
>> -------- 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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> Chimera-users at cgl.ucsf.edu
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