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 <[log in to unmask] <mailto:[log in to unmask]>> 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/
> ___________________________________________
>
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