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 <[email protected]> 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 <[email protected]> *On Behalf Of *Klontz, > Erik > *Sent:* Saturday, February 2, 2019 22:05 > *To:* [email protected] > *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
