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 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/
