Thank you all for your feedback. I received many helpful responses. To summarize them, users might find the following resources helpful:
http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm http://achesym.ibch.poznan.pl http://eppic-web.org http://www.ruppweb.org/new_comp/spacegroup_decoder.htm http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver In my own example, my crystal was C 2 2 21 with unit cell 89.30, 137.12, 264.71, 90, 90, 90 The easiest solution I found to generate the 3x4 translation/rotation matrix was to open the structure in Coot, turn on symmetry mates (Draw-->Cell & Symmetry) and then middle mouse click on the correct chain that completes the biological assembly (or alternatively, File-->Save Symmetry Coordinates-->left click chain). The symmetry operator shows in the bottom left of the window in Coot. In my case, this gave an output of "(X, -Y, -Z) + (0 0 0)" for one, and "(-X, Y, -Z + 1/2) + (-1 0 -1)" for the other. In the 3x4 translation/rotation matrix format required for PDB deposition, these correspond to: Format: R1-1 R1-2 R1-3 T1 R2-1 R2-2 R2-3 T2 R3-1 R3-2 R3-3 T3 Solutions: 1 0 0 0 0 -1 0 0 0 0 -1 0 -1 0 0 -89.3 0 1 0 0 0 0 -1 -132.35 To check your work, you can save the symmetry coordinates and then load them into the ccp4 program "superpose". Superimpose your original PDB onto the symmetry mate. The output contains a rotation matrix and a translation vector that should correspond to the same solution. Thanks everyone! Erik ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Sunday, February 3, 2019 6:21:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies Well - you have one of many examples where your 4 chains do not form the biological tetramer, but as you say there are two half tetramers in the asymmetric unit, I would expect that Pisa has already told you there is an interface between AC and it’s summetry equivalent and told you the symmetry operator that generates this? Look st interfaced output And the same for the BD interface . Lots of haemoobin examples of this. On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp <hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> wrote: The most trivial procedure is probably to generate the symmetry mates in Coot (color by symop makes selection easier), pick the ones completing your known biological assembly, and saving those using File/Save Symmetry Coordinates. Once you have the correct model you can superimpose the dimers in Coot and read the DCM and the translation vector – if that is what you want. If you click any of the atoms in a symop-ed molecule, you get the crystallographic operator and translation. If you want the crystallographic symops in symbolic and matrix format, you can use http://www.ruppweb.org/new_comp/spacegroup_decoder.htm Standard settings only. Best, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Klontz, Erik Sent: Saturday, February 2, 2019 22:05 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
