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<div class="moz-cite-prefix">Hi J-F,<br>
<br>
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.<br>
<br>
Tom<br>
<br>
</div>
<blockquote cite="mid:5081C574.4030104@sonic.net" type="cite">
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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 moz-do-not-send="true"
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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