Hello, it's because your unit cell has a 120 degree angle and cos 120 = -0.5, sin 120 = 0.866. It reminds me of an essay I wrote in the lockdowns:
https://www.ucl.ac.uk/~rmhajc0/frorth.pdf Best wishes, Jon Cooper. [email protected] Sent from Proton Mail Android -------- Original Message -------- On 20/09/2025 14:45, Qixu Cai 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/
