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.. ______________________________________________________________________
