Dear Ian, Herman, and others
What an active and responsive bulletin board!! Thanks for the helpful suggestions - it is going to take me some time to digest and then try to implement something - but I will report back and let you know how I am getting on. Once again, thanks very much for the help! Kind regards James From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ian Tickle Sent: 13 March 2013 15:59 To: [email protected] Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates? Herman, Yes you are right. I was assuming that since these are REMARKs then programs would ignore them and use the space group in the CRYST1 record to define the symmetry operators (a better way in my view, assuming that the space group setting symbol is unambiguous as it should be). If programs are using the SYMTRY info then of course that would also need to be updated. This would be the same transformation as for the other matrices, i.e. Ct = CoT^-1 where Co is the original SYMTRY matrix and Ct is the new one for the transformed co-ords (again 4x4 matrices). Cheers -- Ian On 13 March 2013 15:45, <[email protected]> wrote: Dear Ian, My feeling is that most crystallograpic programs use indeed a separate library with symmetry operators acting on fractional coordinates. However, the SMTRY records in the PDB files work on the orthogonal coordinates and some of the more advanced non-crystallographic viewing/modeling programs use these to generate symmetry mates. In this way, those non-crystallographic programs do not need to provide libraries with symmetry operators and they do not need to bother whether one has a hexagonal or rombohedral settings or whether the space group is P21212 or P22121. If crystallographers would be using these records as well, there would have been a lot less confusion, but that is another story. So to be on the safe side, one would need to either delete or transform the SMTRY records. Cheers, Herman ________________________________ From: Ian Tickle [mailto:[email protected]] Sent: Wednesday, March 13, 2013 4:22 PM To: Schreuder, Herman R&D/DE Cc: [email protected] Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates? On 13 March 2013 14:51, <[email protected]> wrote: As I see it, there is no need to change the orthogonal coordinates. They are used in connection with the SYMTRY records to generate the symmetry mates. Changing the orthogonal coordinates would mean changing the SYMTRY records, which would only complicate things. If we do not change the orthogonal coordinates, we do not need to change the SCALE matrix and the only thing we need to change is the ORIGX matrix. PS note there is no need to change the symmetry operators in either scheme, because these actually operate on the fractional co-ordinates, not directly on the orthogonal ones. In my scheme I redefine the SCALE matrix so that together with the transformed co-ordinates you recover the original fractional co-ordinates and so the symmetry still works correctly (theoretically of course!). Cheers -- Ian ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or [email protected]. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 0000 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________
