[3dem] Euler angle conventions in Spider/Web and other packages
kusser at lmb.uni-muenchen.de
kusser at lmb.uni-muenchen.de
Fri Dec 18 04:24:04 PST 2009
Dear 3DEM members,
do I understand it correctly from what Tapu wrote below that VO EA uses an Euler convention different from SE A and both are yet again different from what WEB uses (and I dont even start talking about JWEB, Chimera or EMAN here)?
Regarding all the fuss about conventions, it would be most lovely to have a Spider script that simply takes the angles from VO EA and rotates the volume such that Chimera displays it upon loading without having to apply any manual rotations, flipping of axes or what have you. Chimera is my personal preference, but it might also be useful for Web or any other visualization tool to have a such script.
Could anyone familiar with the matter of Euler angles sacrifice half an hour to come up with such a script? I'm sure it's a no-brainer for people involved into these convention things and a lot of users would benefit from it... at least I would a great deal.
Tanvir Shaikh wrote:
>> I am trying to make surface representations of a volume in Web. They
>> should be the same view like projections that were used to align the
>> data but it seems that I cannot figure out how to transfer the euler
>> angles from reference angles file coming from the VO EA command (that
>> are then used in PJ 3Q) over to Web to create the surfaces.
> The answer is a bit complicated. I hope you actually mean WEB and not
> JWEB because the answer is different, and different yet again for Chimera,
> The Surface command in WEB, using Euler angles (0,0,0), is not equivalent
> to the projection in SPIDER along (0,0,0). For reason unknown to me,
> WEB reads in the volume along x-axis (from the negative side, I believe)
> normal to the yz-plane.
> In order to get a surface equivalent to SPIDER's (0,0,0) projection, the
> Euler angles in WEB are (90,90,180). If you want to compare the reference
> projections to the respective surfaces, if your projection angles are
> (phi, theta, 0), the angles in WEB need to be (phi+90,90,theta+180).
> (Note that the angles output by VO EA are reversed from the angles that
> one would apply manually, i.e., they are in the form (psi, theta, phi).)
> If angle psi is not zero, there isn't a simple conversion. In this case,
> I'd recommend using command SA E (SumAlign Euler), using (phi,theta,psi)
> as the first set of angles and (90,90,180) as the second.
> If you have more questions, let me know. If I've written anything
> incorrectly, hopefully Dean will correct me.
> -Tapu Shaikh
> IMPORTANT NOTICE: This e-mail and any attachments may contain
> confidential or sensitive information which is, or may be, legally
> privileged or otherwise protected by law from further disclosure. It
> is intended only for the addressee. If you received this in error or
> from someone who was not authorized to send it to you, please do not
> distribute, copy or use it or any attachments. Please notify the
> sender immediately by reply e-mail and delete this from your
> system. Thank you for your cooperation.
More information about the 3dem