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Hi J-F,<br>
<br>
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<br>
<br>
open 3j1z<br>
molmap #0 13<br>
open emdbID:5450<br>
vop localCorrelation #0 #1 windowSize 5 model #2<br>
scolor #1 volume #2 cmap .8,blue:0.9,white:1,red<br>
transparency 30 #1<br>
<br>
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).<br>
<br>
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.<br>
<br>
The new command will be in tonight's daily build.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] coloring 3D maps according to local
cross-correlation fit of docked PDB structures<br>
From: Jean-Francois Menetret <br>
To: Tom Goddard <br>
Date: 10/19/12 8:35 AM<br>
<blockquote type="cite"><font>Hi Tom,<br>
<br>
<font>we <font>would like </font>to<font> color <font>the</font>
surface representation of ou<font>r molecule with the local
correlation score between the fitted atomic models and the
EM<font>-maps<font>; <br>
y</font>ou can find an example <font>in <font>f</font>igure</font></font></font></font>S3
of Hi<font>pp et al. </font></font><font>Nucleic Acids
Research, 2012, Vol. 40, No. 7 3275–3288</font></font><br>
<br>
best wishes<br>
J-F<br>
<br>
<div class="gmail_quote">On Thu, Oct 18, 2012 at 7:37 PM, Tom
Goddard wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi J-F,<br>
<br>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Tom</font></span>
<div>
<div class="h5"><br>
<br>
<br>
-------- Original Message --------<br>
Subject: [Chimera-users] coloring 3D maps according to
local cross-correlation fit of docked PDB structures<br>
From: Jean-Francois Menetret<br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu"
target="_blank">chimera-users@cgl.ucsf.edu</a><br>
Date: 10/18/12 6:24 AM<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite"><font>Dear users,<br>
<font>we would like to </font></font><font><font><font>color
a<font> Cryo-EM map according to the c<font>ross-corr<font>elation
fit of docked PDB structure<font>s.</font><br>
<font>Is that po<font>s<font>sible in
Chimera ?<br>
<font>Best wishes<br>
<font>J-F M<font>enetret</font></font></font></font></font></font></font></font></font></font></font>
</font><br>
</blockquote>
<br>
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