Well done. Sorry for the many typos, but they don't seem to have slowed you down any! eab
On 07/07/2015 11:25 AM, Tobias Beck wrote:
Dear all, Thanks for your helpful emails. Here is a short summary: I followed Edward Berry's suggestions. Unfortunately I could not use any superposition to the new structure, as suggested by some, since the structures are too different. I used lsqman and mama to obtain the sperical polars for my twofold as pointed out by Ed. After this, I rotated my structure in two steps based on these angles, but using rotation matrixes in the form cos_theta -sin_theta 0 sin_theta cos_theta 0 0 0 1 as pointed out by Ed, to align the twofold axis in my structure to a twofold axis in the new space group. That was done in pdbset (I did not need to consider translation in my case). Thanks again for helping me! Best wishes, Tobias. On Fri, Jun 19, 2015 at 4:54 PM, Edward A. Berry <ber...@upstate.edu <mailto:ber...@upstate.edu>> wrote: A number of superposition programs allow to superimpose specified atoms (such as CA). Once you get the operator, comparing two different operators is not a job for a conventional superposition program, since you are superimposing a line on a line which has the extra degree of freedom- rotation about the line. If you express the operator in spherical polar coordinates, which the superposition program may provide or you can get from the matrix using ccp4 "rotmat", you should be able to work out the relation between the axes. Using the Uppsala sofware factory programs: #This is superimposing parts of chains C, A, B on P, N, O (and vice versa - it's proper 2-fold) lsqman -b <<eof chain_mode original re m1 cbc596.pdb exp m1 C20-370 P20-370 A20-200 A250-400 B30-200 B250-400 N20-200 N250-400 O30-200 O250-400 m1 P20 C20 N20 N250 O30 O250 A20 A250 B30 B250 save m1 m1 ncsasc01.odb quit eof This prints the operator and saves it in ncsasc01.odb* ---------------- - The 2010 atoms have an RMS distance of 0.130 A - RMS delta B = 15.367 A2 - Corr. coeff. = 0.6601 - Rotation : -0.834671 <tel:0.834671> -0.550747 -0.001321 <tel:0.550747%20-0.001321> - -0.550747 <tel:0.550747> 0.834660 0.004400 <tel:0.834660%20%200.004400> - -0.001321 0.004400 -0.999989 <tel:0.999989> - Translation : 129.384 38.428 171.594 ------------------- Now use mama in an off-label way to convert to polar coordinates: mama overlap ncs ncsasc01.odb gives: --------------------------- - RT-OP 1 = -0.8346710 <tel:0.8346710> -0.5507473 <tel:0.5507473> -0.0013208 129.384 - -0.5507473 <tel:0.5507473> 0.8346604 <tel:0.8346604> 0.0044000 38.428 - -0.0013208 0.0044000 -0.9999894 <tel:0.9999894> 171.594 - Determinant of rotation matrix 1.000000 - Column-vector products (12,13,23) 0.000000 0.000000 0.000000 - Crowther Alpha Beta Gamma 106.709 179.736 73.291 - ***Spherical polars Omega Phi Chi 90.132 -73.291 180.000*** - Direction cosines of rotation axis 0.287514 <tel:0.287514> -0.957774 -0.002303 <tel:0.957774%20%20%20-0.002303> - X-PLOR polars Phi Psi Kappa *undefined* *undefined* 180.000 - Lattmann Theta+ Theta2 Theta- -180.000 179.736 -146.582 - Rotation angle 180.000 ------------------------- * if you use the .odb file outside of the USF software, be aware the matrix is the transpose (or more accurately it is written by columns). In ccp4 this is taken care of withthe keyword "odb". On 06/19/2015 09:07 AM, Tobias Beck wrote: Dear all, I have a PDB file that contains NCS in the asymmetric unit, probably point group D3. 1.) What program is recommended for determining the symmetry operators from PDB coordinates? I found findncs, but this uses only heavy atom coordinates (I could probably use just the sulfurs from the PDB as a work around). 2.) Then I would like to compare the PDB file to a related structure. Here I would like to align the symmetry operators determined above with symmetry elements found in a different space group, for example align the twofold axis from NCS with a twofold axis in found in a particular space group. What is a good way to go about this? I am aware that NCS is used in programs as restraints during refinement, but here I am interested in obtaining the NCS symmetry operators and aligning them to symmetry elements present in a new space group. Maybe I am overlooking an obvious solution. Any help is greatly appreciated. Thanks and best wishes, Tobias. -- ___________________________________________ Dr. Tobias Beck - independent group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 <tel:%2B49-241-80-90057> fax: +49-241-80-99003 <tel:%2B49-241-80-99003> web: http://www.ac.rwth-aachen.de/extern/beck/ ___________________________________________ -- ___________________________________________ Dr. Tobias Beck - independent group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___________________________________________
