[Chimera-users] Measure translation of two domains?

Oliver Clarke olibclarke at gmail.com
Tue Jul 7 16:04:27 PDT 2015


Hi all, 

I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation.

I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. 

What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output?

Cheers,
Oliver.

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