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Hi Ed,<br>
<br>
Yeah for chains A and B in a single PDB file use<br>
<br>
match :.A :.B move false show true<br>
<br>
which will report in the reply log<br>
<br>
Motion from original file coordinates<br>
Matrix rotation and translation<br>
0.86421485 0.50312170 -0.00112044 0.02930667<br>
-0.50311880 0.86421463 0.00213137 0.02433383<br>
0.00204064 -0.00127825 0.99999710 48.44760893<br>
Axis -0.00338844 -0.00314144 -0.99998932<br>
Axis point -0.30430942 0.18590569 0.00000000<br>
Rotation angle (degrees) 30.20700574<br>
Shift along axis -48.44726749<br>
<br>
This requires a Chimera daily build<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/download.html#daily">http://www.cgl.ucsf.edu/chimera/download.html#daily</a><br>
<br>
since the 1 year old production release (1.5.3) does not allow
matching two parts of the same molecule.<br>
<br>
The above will only work if chains A and B have identical atoms.
If they differ in any way you can try specifying equivalent sets of
atoms, for example CA only, "match :.A@CA :.B@CA move false show
true". If the sequences differ then you will need to use MatchMaker
and it still requires two separate models and you could use two
copies of the same PDB file.<br>
<br>
Sorry I read your original question too quickly.<br>
<br>
Tom<br>
<br>
<br>
<blockquote cite="mid:4F0CD01A.8090907@virginia.edu" type="cite">
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<font face="Times New Roman, Times, serif">Hi,<br>
There is actually no map involved. The PDB coordinate system
has the axis at x=0, y=0 (along z). I am not trying to fit
these, only to look at the angles within this PDB file.<br>
Regards,<br>
Ed<br>
</font><br>
On 1/10/2012 6:31 PM, Tom Goddard wrote:
<blockquote cite="mid:4F0CCA61.1010705@sonic.net" type="cite">
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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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<br>
</blockquote>
<br>
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