Shane, After you define which segments share proper or improper all NCS their parameters in MAIN environment, they will be calculated and stored in such macro files.
$ cat mol_A_to_B.com ! SAVING RMS FIT DATA: set matrix MAT_ROT number - 0.959598 -0.031620 -0.279592 - -0.029443 0.976927 -0.211536 - 0.279830 0.211222 0.936526 set vari XTRAN global real = 3.66 set vari YTRAN global real = 105.12 set vari ZTRAN global real = -33.40 return If you want to renormalize your matrices, you not only need to ensure that the length of your lines or columns is equal to 1, but also that they are orthogonal to each other, which is the easiest achieved by calculating the cross products of the matrix lines (a,b,c): (a * b = c ) through which you calculate first c and then either a or b. I would not do it, because the limited precision distorts the transformation and making in orthogonal will distort the accuracy of superimposition. best, dusan > On Apr 3, 2015, at 1:00 AM, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > > Date: Wed, 1 Apr 2015 20:47:25 -0400 > From: Shane Caldwell <shane.caldwel...@gmail.com> > Subject: Re: Sortwater NCS Matrix input > > Alright, thanks! It's a good thing, then, I spent the afternoon brushing up > on matrices. > > I guess the next, probably more general question for the bb is: which > utilities export an NCS transformation matrix with more precision? > *superpose* and *gesamt* only export three decimals, though I'm sure they > use greater precision under the hood. I'm not opposed to exporting from > coot or pymol either, I just haven't figured out how to do this yet - what > would be the simplest way to calculate and export an NCS transformation > matrix? > > Shane > Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
