The pdb matrix is the equivalent of your matrix, but in the orthogonal axial system.. Yours is correct for the crystal axial system.. OK? Eleanor
On Sat, 20 Sept 2025 at 14:45, Qixu Cai < [email protected]> wrote: > Dear Thierry, > > Thank you for your reply. > After I provided the symmetric operator to PDB staff, they updated the > matrix as below: > -0.500000 -0.866025 0.000000 89.06300 > -0.866025 0.500000 0.000000 51.42055 > 0.000000 0.000000 -1.000000 46.27767 > The matrix is totally different with the matrix I provided. How was the > symmetric operator (-X+2/3,-X+Y+1/3,-Z+1/3) transformed to the above matrix? > The space group is H32 with cell constents of 178.126 178.126 138.833 > 90.00 90.00 120.00. > > Thanks and best regards, > Qixu Cai > Email: [email protected] > > > > Fischmann, Thierry <[email protected]> 于2025年9月19日周五 23:37写道： > >> Hi, >> >> >> >> The matrix is correct for the operator you provide. >> >> >> >> Thierry >> >> >> >> *From:* CCP4 bulletin board <[email protected]> *On Behalf Of *Qixu >> Cai >> *Sent:* Friday, September 19, 2025 11:30 AM >> *To:* [email protected] >> *Subject:* [ccp4bb] convert symmetric operator to matrix & coot1 >> >> >> >> You don't often get email from >> [email protected]. Learn why this is >> important <https://aka.ms/LearnAboutSenderIdentification> >> >> *EXTERNAL EMAIL*– Use caution with any links or file attachments. >> >> Dear all, >> >> >> >> There is a dimer in the asymmetric unit of a structure, and applying the >> symmetric operator (-X+2/3,-X+Y+1/3,-Z+1/3) can generate a tetramer, which >> is a biological assembly. When I deposit the structure to PDB, I need to >> provide a matrix to generate the biological assembly. Is the following >> matrix correct for pdb format? >> >> -1 0 0 0.6667 >> >> -1 1 0 0.3333 >> >> 0 0 -1 0.3333 >> >> >> >> Another question is that I can use "Calculate --> Modelling --> New >> molecule from symmetry op..." to generate new molecule in wincoot0.9.8. >> However, I cannot find similar function in new wincoot1.18. I also found >> that many useful functions in "Calculate --> Modelling" of coot0.9.8 are >> not available in coot1. Will they come back in the following versions of >> coot1? >> >> >> >> Thanks and best regards, >> >> >> >> Qixu Cai >> Email: [email protected] >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This e-mail message, together with any attachments, contains information >> of Merck & Co., Inc.,Rahway, NJ, USA, and/or its affiliates, known as MSD >> outside of the United States and Canada, that may be confidential, >> proprietary, copyrighted and/or legally privileged. (Direct contact >> information for affiliates is available at - Contact us - MSD >> <https://www.msd.com/contact-us/>.) It is intended solely for the use >> of the individual or entity named on this message. If you are not the >> intended recipient, and have received this message in error, please notify >> us immediately by reply e-mail and then delete it from your system. >> >> > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
