Re: [COOT] Map rotation and translation
Thank you Paul for the explanation/clarification. Indeed, it would be enough for me at the moment if I could align maps according to the fit I get in ChimeraX. The "transform_map() function" sounds exactely like what I was looking for! Could you perhaps elaborate if I filled in the parameters correctly (see below)? ChimeraX output: Fit map job122_class1 in map job145_class1+3 using 378391 points correlation = 0.9626, correlation about mean = 0.8182, overlap = 1.076e+04 steps = 40, shift = 0.009, angle = 0.00377 degrees Position of job122_class1 (#1) relative to job145_class1+3 (#4) coordinates: Matrix rotation and translation 0.3251 -0.00473394 -0.01060925 2.07918736 0.00471099 0.8651 -0.00218664 -0.57281865 0.01061946 0.00213651 0.4133 -1.65452589 Axis 0.18292243 -0.89823687 0.39963723 Axis point 165.64873479 0. 190.89655799 Rotation angle (degrees) 0.67707290 Shift along axis 0.23364667 Coot command: Based on |(transform-map /imol/ /rotation-matrix/ /trans/ /point radius/)| from the user manual: (transform-map 1 (list 0.3251 -0.00473394 -0.01060925 0.00471099 0.8651 -0.00218664 0.01061946 0.00213651 0.4133) (list 2.07918736 -0.57281865 -1.65452589) (list 181.1739959716797 205.94700622558594 198.18699645996094) 10) The value for "point" I took from running |(rotation-centre)| in Coot, is that correct? The resulting map fragment seems to be aligned quite well to the resampled map.| | I set the radius to 10 for testing purposes, is there a way to use the full map by default? Best, Helge To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Map rotation and translation
Paul, both your emails are partly correct. Rotation+translation, called skew transformation (words 25-37) is supported by CCP4 maplib and PyMOL. It's mentioned in the MRC/CCP4 2000 specification on CCP-EM page: https://www.ccpem.ac.uk/mrc_format/mrc2000.php although it's not mentioned in the 2014 version of this spec. I don't know if any program apart from PyMOL is using it. When Tom wrote about the shift of origin, he must have meant N[XYZ]START fields. Marcin On Fri, Jan 28, 2022 at 6:00 AM Paul Emsley wrote: > > On 27/01/2022 01:13, Paul Emsley wrote: > > > > Alas, I have not done what I think you want (which is to say, to use > > the extented CCP4/MRC map header information to represent an arbitrary > > rotation/translation). > > > > After having read Tom's reply about these > rotation/translation/interpolation issues on the ChimeraX mailing list > I'd like to correct a misunderstanding I had about what Coot wasn't > doing. There is an unused (by Coot) slot in the CCP4/MRC map header, I > had thought that the slot allows rotation and translation but it does > not - it allows a shift of origin (translation) only. Everything Tom > said was on the money. > > Paul. > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list > hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
