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<blockquote cite="mid:4F0CBE7D.3000504@virginia.edu" type="cite"> <font
face="Times New Roman, Times, serif">Hi,<br>
It is not obvious to me if there is a simple way to do this in
Chimera. Given a PDB file containing a number of chains of
identical molecules arranged into a helix, but without exact
helical symmetry, is there some way to measure the rotation
between adjacent chains? I imagine that I can use MatchMaker,
and then convert the resulting rotation matrix to the angle
about the helical axis...<br>
Regards,<br>
Ed</font><br>
</blockquote>
<br>
Hi Ed,<br>
<br>
If PDB models #1 and #2 are fit to a filament map you can use
Chimera command<br>
<br>
measure rotation #1 #2<br>
<br>
which will produce output in the Reply Log (menu Favorites / Reply
Log) like<br>
<br>
Position of 1mwk (#2) relative to 1mwk (#1) coordinates:<br>
Matrix rotation and translation<br>
0.89907669 -0.42653054 -0.09865501 -14.80260678<br>
0.38452015 0.87709721 -0.28782762 9.59677669<br>
0.20929731 0.22084426 0.95258724 -47.13790770<br>
Axis 0.50580078 -0.30621414 0.80647286<br>
Axis point 19.41814624 18.14474471 -0.00000000<br>
Rotation angle (degrees) 30.18795070<br>
Shift along axis -48.44128198<br>
<br>
This specifies the rotation in PDB #1 coordinates, not the
coordinates of the map these two molecules have been fit into. It
is described as a 3x3 rotation matrix and a translation (4th column
of above matrix). And it is equivalently described as an axis,
point on the axis, rotation angle and shift along the axis. The
command will also show in the graphics window the axis of rotation
for this latter specification.<br>
<br>
Unfortunately there is not an option to express this rotation in the
map coordinate system which is probably what you are interested in.
Here's a way to do that though. Fit the first molecule in the map.
Then write out that PDB file using the map coordinates using Chimera
menu File / Save PDB... with the "Relative to model mymap.mrc"
option enabled. Now close that fit molecule and open the saved
PDB. It has the same coordinate system as the map. Open a second
copy of that PDB and fit it in another position in the map. Then
use the "measure rotation #1 #2" command (can be shortened to "me
rot #1 #2").<br>
<br>
I'll see if I can easily add an option to the measure rotation
command to report the result in the map coordinate system.<br>
<br>
Tom<br>
<br>
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