-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear James,
if I understand correctly you want to transform structure B onto structure A and then compare the crystallographic packing of A and B. I might be wrong, but I think the most convenient way for the users would be a display program which can handle two different global coordinate systems (that of A and that of B) so that the symmetry operators of B recreate the original crystal packing of B _after_ it was mapped onto A. I am not aware of a program which handles such two different global coordinate systems, and if I am correct your last assumption is correct: you have to "[..] accept that my aligned coordinates should no longer be expected to recreate the packing environment [...]" If you want to keep track within the PDB-file, maybe for later reference, you could just add REMARK cards that explain what you did, i.e. contain the original PDB-ID, transformation operator and the reference PDB-ID. As a work-around in case I did understand you correctly, you could save the contacting symmetry equivalents of B into its own PDB file (e.g. in coot) _before_ the transformation, then apply the transformation so that the contacting molecules are transformed the same way as B. If somebody has a shorter way, I am happy to learn. Best regards, Tim On 03/13/2013 01:57 PM, James Davidson wrote: > Dear All, > > > > This is my first post to the group - so "Hello"! I have searched > with not much success to find an answer to my question, so I > thought I would try posting here for some expert advice. > > I should start by saying that I am not a crystallographer, but > please don't hold that against me! > > > > I am working with PDB files that are being aligned to reference > structures, indirectly by (a) using the alignment tools in PyMOL, > then (b) extracting the transformation matrix and re-applying this > to the ATOM / HETATM entries outside of PyMOL (to avoid atom > reordering / atom charging / etc that occurs when directly > exporting from PyMOL). Anyway, what I wanted to know is is there a > way that I could (or should?) reference that the PDB file > coordinates have been transformed? Is there a way of preserving > the ability of tools (eg PyMOL) to legitimately recreate the > symmetry mates from the transformed coordinates if I eg apply the > same transform to some of the data in CRYST1 and SCALE1, SCALE2, > SCALE3? Or should I instead be adding ORIGX1, ORIGX2, ORIGX3 > entries to show that a transformation has been applied? Or, > indeed, should I just accept that my aligned coordinates should no > longer be expected to recreate the packing environment? > > > > I have read through what I think is the correct section of the PDB > documentation, but I must confess that my lack of expertise means > I am in danger of approaching an old(?) problem through naïve trial > and error! > > > > Any help / advice greatly appreciated. > > > > Kind regards > > > > James > > > ______________________________________________________________________ > > > 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.. > ______________________________________________________________________ - -- > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRQIqFUxlJ7aRr7hoRAkJtAJ0Xt/HX2ptpvV6Dk59lme9wDllPrgCg83um YfBTeC8MRbOmomq/CUUCtcw= =PUZE -----END PGP SIGNATURE-----
