Hi,
> 1) I have a map which was autorefined with no symmetry. The resulting structure has approximate C2 symmetry. (I.e. it's a psuedo-dimer). If I run relion_align_symmetry it finds the ~C2 axis nicely and reports the corresponding Euler angles. However, if I project the symmetry aligned map along rot=0, tilt=0, phi=0 and compare that with the projection of the original map using the angles reported by relion_align_symmetry, the 2 projections are translated slightly (~1 pixel) with respect to each other in both x and y. They seem to be identical except for this translation. Can someone please explain the origin of this and hopefully tell me how to avoid it?
I don't know. "relion_align_symmetry" was developed for "rough"
alignment of low resolution maps coming from initial model generation.
If you need high accuracy, I recommend other tools, for example,
ProSHADE in CCPEM. It is more accurate and fast.
> 2) Given the star file from the original refinement and the Euler angles from relion_align_symmetry, I'd like to generate a new star file corresponding to a the reference now having it's axes C2 aligned. Are there any command-line utilites in Relion which will do perform this transformation easily? (Certainly I can compute rotation matrices, multiply, and convert back to Euler angles if necessary. I'm just wondering if there's an easier way already provided which I've overlooked...
No. I would simply refine again with the reference in your preferred
pose.
Best regards,
Takanori Nakane
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|