Re: [ccp4bb] convert orientation matrix format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Almudena, depending on your application there might be a different approach from what I suggested before: you could use my 'spots4cellnow' (http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/spots4cellnow/) to convert the SPOTS.XDS into reciprocal coordinates (it only applies the maths from W. Kabsch, Acta Crystallogr. D66 (2010), pp 133-144). The output can be read by cell_now which you have access to if you have access to saint / apex. cell_now writes a p4p file including the orientation matrix. This should be a work-around if the transformation does not fit. Best, Tim On 11/05/2013 02:29 PM, Almudena Ponce Salvatierra wrote: Hi everyone, I would like to know how to change matrix format from the one I get out of XDS to the one that comes out of SAINTS. Or the other way around. My question is: is the beam along the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSexI0UxlJ7aRr7hoRAqKiAKDu1ONYykRkAU0ZGZsqCAWJQR8NZACg8uvV EZl/PdpZ4YrlXi4rcD5tqCM= =G2Yg -END PGP SIGNATURE-
[ccp4bb] convert orientation matrix format
Hi everyone, I would like to know how to change matrix format from the one I get out of XDS to the one that comes out of SAINTS. Or the other way around. My question is: is the beam along the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena.
Re: [ccp4bb] convert orientation matrix format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Almudena, if I understand either documentation correctly, you have to multiply the XDS orientation matrix (from XPARM.XDS) from the left with [ 00 1 ] [ - 1 0 0 ] [ 0 - 1 0 ] (the z-axis in XDS becomes the x-axis in saint; the x-axis in XDS becomes y-axis in saint in opposite direction; the y-axis in XDS becomes the z-axis in saint in opposite direction). This provides you with a matrix ax ay az bx by bz cx cy cz i.e. row-wise the directions of a, b, and c in the saint coordinate system. - From a, b, and c you can calculate V = a.(b^c) and a*=(b ^ c)/V b*=(c ^ a)/V c*=(a ^ b)/V The saint matrix has these values column wise, i.e. a matrix a*_x b*_x c*_x a*_y b*_y c*_y a*_z b*_z c*_z The maths are easily done with the program maxima, once you know the syntax: bb: matrix([ 0,0,1], [-1,0,0], [0,-1,0]); a: [-2.372110 , 1.479120, -10.597644]; b: [-12.481461, 2.100587,1.965943]; c: [ -2.525253, 17.465330, -0.015521]; V: a.(b ~ c); astar: (b ~ c)/V; # etc. Good luck, Tim On 11/05/2013 02:29 PM, Almudena Ponce Salvatierra wrote: Hi everyone, I would like to know how to change matrix format from the one I get out of XDS to the one that comes out of SAINTS. Or the other way around. My question is: is the beam along the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSeQePUxlJ7aRr7hoRAurVAJ41QHZeFUZqWUexos+zyCNB/L6BlgCg7d8c 53iIruByCN8erxIEWFc+AT0= =/L9B -END PGP SIGNATURE-
Re: [ccp4bb] convert orientation matrix format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry for the misleading example for the maxima code: you have to create a matrix from a,b,c (X: matrix(a,b,c)) and left-multiply it with the matrix bb in order to make the coordinate transformation. Best, Tim On 11/05/2013 03:58 PM, Tim Gruene wrote: Dear Almudena, if I understand either documentation correctly, you have to multiply the XDS orientation matrix (from XPARM.XDS) from the left with [ 00 1 ] [ - 1 0 0 ] [ 0 - 1 0 ] (the z-axis in XDS becomes the x-axis in saint; the x-axis in XDS becomes y-axis in saint in opposite direction; the y-axis in XDS becomes the z-axis in saint in opposite direction). This provides you with a matrix ax ay az bx by bz cx cy cz i.e. row-wise the directions of a, b, and c in the saint coordinate system. - From a, b, and c you can calculate V = a.(b^c) and a*=(b ^ c)/V b*=(c ^ a)/V c*=(a ^ b)/V The saint matrix has these values column wise, i.e. a matrix a*_x b*_x c*_x a*_y b*_y c*_y a*_z b*_z c*_z The maths are easily done with the program maxima, once you know the syntax: bb: matrix([ 0,0,1], [-1,0,0], [0,-1,0]); a: [-2.372110 , 1.479120, -10.597644]; b: [-12.481461, 2.100587, 1.965943]; c: [ -2.525253, 17.465330, -0.015521]; V: a.(b ~ c); astar: (b ~ c)/V; # etc. Good luck, Tim On 11/05/2013 02:29 PM, Almudena Ponce Salvatierra wrote: Hi everyone, I would like to know how to change matrix format from the one I get out of XDS to the one that comes out of SAINTS. Or the other way around. My question is: is the beam along the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSeQnEUxlJ7aRr7hoRAly0AKDaSKZG69m/voWIy8Cwd2sTILuHJgCfQAdo zukXtgxBdwhBZCqE3YXJayM= =Y7/D -END PGP SIGNATURE-
