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Thank you Elaine.</div>
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This helps.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 26 November 2021 17:15<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] measuring rotation between two homologous PDB models</font>
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<div class="PlainText">Hi Yaikhomba,<br>
Measure rotation is simply telling you how #1 was already moved when it was matched to #2. It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains. I tried to explain this
in the help, but I know it's confusing:<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation</a>><br>
<br>
If I understand correctly here is how I might try to do it:<br>
<br>
(1) superimpose 6gj2 onto 6rfr like you did already<br>
(2) save PDB 6gj2 relative to 6rfr (in matched position)<br>
(3) close 6gj2<br>
(4) reopen saved version of 6gj2 that is already matched on 6rfr<br>
(5) then superimpose those domains<br>
(6) then measure rotation<br>
<br>
E.g. commands something like this:<br>
<br>
open 6g2j; open 6rfr<br>
match #1/L,N to #2/5,4 pair ss<br>
save 6g2jnew.pdb #1 rel #2<br>
close #1<br>
open 6g2jnew.pdb<br>
match #1/F to #2/B<br>
measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true<br>
<br>
That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind. I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Nov 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Elaine and ChimeraX Team<br>
> <br>
> My query relates to measuring rotation between two subunits from homologous models in ChimeraX.<br>
> <br>
> Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift.<br>
> So,<br>
> • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr).<br>
> • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr).<br>
> I am using the following commands:<br>
> -- open 6g2j; open 6rfr;<br>
> -- match #1/L,N to #2/5,4 pair ss;<br>
> -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;<br>
> <br>
> The log report is:<br>
> Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system:<br>
> Matrix rotation and translation<br>
> 0.80441124 0.40360431 -0.43591986 67.76279700<br>
> 0.18783349 0.52334489 0.83116106 -121.82969657<br>
> 0.56359661 -0.75047565 0.34517410 202.31442783<br>
> Axis -0.83978100 -0.53070022 -0.11456502<br>
> Axis point 0.00000000 87.13355460 206.39866592<br>
> Rotation angle (degrees) 70.33834463<br>
> Shift along axis -15.42901832<br>
> <br>
> Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong.
<br>
> Could you please help?<br>
> <br>
> Thanks<br>
> Yaikhomba<br>
<br>
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