Re: [ccp4bb] determine NCS operators from PDB coordinates
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_theta0 sin_thetacos_theta0 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 of0.130 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 -0.89 tel:0.89 - Translation :129.38438.428 171.594 --- 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 -0.0013208129.384 - -0.5507473 tel:0.5507473 0.8346604 tel:0.8346604 0.0044000 38.428 - -0.00132080.0044000 -0.894 tel:0.894 171.594 - Determinant of rotation matrix 1.00 - Column-vector products (12,13,23) 0.000.000.00 - 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. -- ___
Re: [ccp4bb] determine NCS operators from PDB coordinates
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_theta0 sin_thetacos_theta0 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 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 of0.130 A - RMS delta B = 15.367 A2 - Corr. coeff. = 0.6601 - Rotation: -0.834671 -0.550747 -0.001321 --0.550747 0.834660 0.004400 --0.001321 0.004400 -0.89 - Translation :129.38438.428 171.594 --- Now use mama in an off-label way to convert to polar coordinates: mama overlap ncs ncsasc01.odb gives: --- - RT-OP 1 =-0.8346710 -0.5507473 -0.0013208 129.384 - -0.55074730.83466040.0044000 38.428 - -0.00132080.0044000 -0.894 171.594 - Determinant of rotation matrix 1.00 - Column-vector products (12,13,23) 0.000.000.00 - 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 -0.957774 -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 fax: +49-241-80-99003 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/
[ccp4bb] determine NCS operators from PDB coordinates
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 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___
Re: [ccp4bb] AW: [ccp4bb] determine NCS operators from PDB coordinates
Well - I would begin by submitting both sets of coordinates to pisa which will attempt to group the NCS into the best complex. Once you have that you can use any of the SUPERPOSE options to fit A to B, A to C , B to C etc. for each molecule and from that deduce your NCS class. eg: Hexamers - 6 fold rotations- teramers - 2 2 2 symmetry etc etc.. Then SSM will probably fit the two different structures together and you can see where the differences are Eleanor On 19 June 2015 at 14:46, herman.schreu...@sanofi.com wrote: Dear Tobias, If you have coordinates available for the different space groups, the obvious solution is to first generate complete NCS units in the different space groups, using appropriate crystallographic symmetry and then superimpose the whole unit with something like lsqkabs. You have to watch out though, that equivalent molecules are used for the superposition. Best, Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Tobias Beck *Gesendet:* Freitag, 19. Juni 2015 15:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] determine NCS operators from PDB coordinates 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 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___
Re: [ccp4bb] determine NCS operators from PDB coordinates
phenix.simple_ncs_from_pdb will detect NCS from input PDB file, write out NCS operators (matrices) and atom selections for NCS related groups. On Fri, Jun 19, 2015 at 6:07 AM, Tobias Beck tobiasb...@gmail.com 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 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___
Re: [ccp4bb] determine NCS operators from PDB coordinates
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 of0.130 A - RMS delta B = 15.367 A2 - Corr. coeff. = 0.6601 - Rotation: -0.834671 -0.550747 -0.001321 --0.550747 0.834660 0.004400 --0.001321 0.004400 -0.89 - Translation :129.38438.428 171.594 --- Now use mama in an off-label way to convert to polar coordinates: mama overlap ncs ncsasc01.odb gives: --- - RT-OP 1 =-0.8346710 -0.5507473 -0.0013208129.384 - -0.55074730.83466040.0044000 38.428 - -0.00132080.0044000 -0.894171.594 - Determinant of rotation matrix 1.00 - Column-vector products (12,13,23) 0.000.000.00 - 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 -0.957774 -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 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___
