But you know that each rotation matrix still only fits one semi-tetramer to its symmetry partner?
Eleanor On Sun, 3 Feb 2019 at 16:54, Klontz, Erik <erik.klo...@som.umaryland.edu> wrote: > 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> > 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> *On Behalf Of *Klontz, > Erik > *Sent:* Saturday, February 2, 2019 22:05 > *To:* 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
