Hi Eric, You can lookup the symmetry operator in the International Tables (http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm). Alternatively, you can use coot to find the crystallographic symmetry operator that generates the second half of your tetramer.
Draw/Cell & Symmetry and then generate the symmetry mates. Select File/Save Symmetry Coordinates Click on the right symmetry mate. Coot will display the symmetry operator in the panel below the viewport of the GUI. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 e-mail: [email protected] <mailto:[email protected]> Faculty webpage: https://tinyurl.com/BMBmooers Google Scholar: https://tinyurl.com/GSbmooers X-ray lab (LBSF): https://tinyurl.com/ouhsclbsf SSRL-LCLS User Meeting: https://conf.slac.stanford.edu/ssrl-lcls-2018/ EasyPyMOL: https://github.com/MooersLab Molecular Graphics Course Links: https://tinyurl.com/molgr Small Angle Scattering Links: https://tinyurl.com/ouhscsaxs ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Klontz, Erik [[email protected]] Sent: Saturday, February 02, 2019 3:04 PM To: [email protected] Subject: [EXTERNAL] [ccp4bb] Generating rotation/translation matrices for biological assemblies Hi all, I'm working on a protein that I believe is tetrameric based on AUC, gel filtration, and crystallography. However, although my asymmetric unit has 4 chains, I cannot form the tetramer within the asymmetric unit. Instead, the asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is completed by pairing up with another half-tetramer from a symmetry mate. If I load this structure into PISA, it recognizes that each of the 'dimers' forms a stable assembly, but cannot seem to assemble the tetramer. However, if I the generate symmetry mates in pymol to create a new PDB for the biological tetramer and give this to PISA, it recognizes a stable tetramer. Specifically, chains A and C in the original PDB pair with chains A and C of the second symmetry mate generated in pymol, while chains B and D in the original pair with chains B and D of the third symmetry mate. How do I use this knowledge to generate a 3x4 rotation with translation matrix for PDB deposition? Thanks, Erik Klontz ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFAw&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=l-idh0jTVr4bPdlB8Zja2txy9RQ71PviMhwJW5u_IR0&s=fNTIXygq_r8IfPM076LWamBA913ke5dtAa54k4dhQLY&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
