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hi Elaine</div>
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thanks for your response.</div>
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Yes I think I am using the command correctly. Sometimes it works but other times it doesn't, so there is clearly something I am missing. It seems arbitrary why it works sometimes and not others, and then why the axis seems to be positioned near my protein
or other times about 50 protein lengths away. It's baffling.</div>
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But yes my protein is helical, so imagine you have actin. I load the map and the model for 1 subunit. I then clone the subunit and fit it into the adjacent position then ask what the rotation is between those two models. As I said it sometimes works, but
not always. Just wondering what it is I could be doing wrong. I alway position the model in the center of the box, I try loading model or map first to see if results vary. Nothing seems to help. Why does the axis appear way off to the side in some cases?</div>
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thanks again</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> Monday, May 11, 2020 2:23 PM<br>
<b>To:</b> Jesse M. Hansen <jhansen6@uw.edu><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] measure rotation</font>
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<div class="PlainText">Hi Jesse,<br>
I'm not sure, but it *might* be a misunderstanding of what this command does. <br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a>><br>
<br>
This command does not evaluate how to best fit or match the two models. It reports the current rotation and translation between the coordinate systems of the two models, which would be zero unless one model was moved relative to the other, either manually or
with some other tool or command such as Fit in Map, match, or matchmaker. (Moving everything collectively, such as rotating or zooming to get a better view, does not change the positions of models relative to each other.)<br>
<br>
Centering just moves the view and doesn't change the coordinates of the structure.<br>
<br>
Imagine you have two copies of the protein, one before fitting and one after fitting. Is the rotation between the two really around an axis that falls inside the protein?<br>
<br>
I may have misapprehended the situation, but this command is commonly misunderstood.<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>
<br>
<br>
<br>
> On May 8, 2020, at 3:38 PM, Jesse M. Hansen <jhansen6@uw.edu> wrote:<br>
> <br>
> hi<br>
> <br>
> I repeatedly have this issue and no idea how to fix it. I send the same files to colleague and they cannot reproduce it. We cannot figure out whether it's some minor detail I am doing, or it's my version of chimera.<br>
> <br>
> When I try "measure rotation #1 #2" the axis ends up either pretty off center or WAY far away (like 20 protein widths away).
<br>
> <br>
> have tried:<br>
> • centering volume and resaving, fitting models into map and resaving. Opening and all looks correct.
<br>
> • tried opening pdb first then maps, or maps first then pdb. Both seem to give different results but neither are precisely down the actual axis of my helical protein despite having centered it.<br>
> • adding "coordinateSystem #" to the command has no effect. The axis that appears is now as long as my box, but it's still not centered<br>
> <br>
> thanks<br>
> Jesse<br>
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