Dear all, I am forwarding to the BB this message from Maksymilian Chruszcz (with his permission), given that his own attempt at posting it directly was not successful.
With best wishes, Gerard. ----- Forwarded message from Maksymilian Chruszcz <m...@cms.mail.virginia.edu> ----- Date: Sat, 07 Mar 2009 11:56:55 -0500 From: Maksymilian Chruszcz <m...@cms.mail.virginia.edu> Subject: Re: Checking for gremlins in deposited diffraction data To: g...@globalphasing.com, ccp4bb@jiscmail.ac.uk Cc: "Dauter, Zbigniew" <zdau...@anl.gov>, Zbyszek Otwinowski <zbys...@work.swmed.edu>, Wladek Minor <wla...@iwonka.med.virginia.edu> X-Mailer: CommuniGate Pro WebUser v5.1.14 Dear Gerard, Thank you very much for turning our attention to structure factors deposited for 3FTT. Preliminary check of our data confirmed your suggestion about F_calc and ph_calc being reported instead of F_meas_au and F_meas_sigma_au respectively. This error was introduced during the conversion from MTZ to CIF file. We are currently discussing with PDB source of such error. Currently I do not know why these particular column were extracted, and I am guessing that maybe PDB scripts handling new mtz files have problems. From: http://pdb-extract.rcsb.org/auto-check/help/checksform.html#conversions 'An automatic conversion is used to convert one standardized SF format to another. If you are using one of the accepted formats (column labels, etc.), and you have made no manual changes to the structure file format yourself, then this method will work for you. Our tool is programmed to recognize which columns correspond to each parameter (depending on the program's format) and "automatically" converts the data to the new format accordingly.' Looks that automatic conversion by PDB was broken by recent change in CCP4 default naming of mtz columns. Please note that authors of a deposit do not get file with structure factors converted from mtz to cif format. They are asked if pdb and mmcif files with coordinates are correct, but this is not a case for structure factors. Maybe it is worth to change PDB policy and ask PDB to send structure factors together with coordinates for authorsÂ’ approval. I will let you know what was source of the error when it will be clarified with PDB. Your suggestion to deposit diffraction images is very good. Actually CSGID puts the server that will make accessible all diffraction images for PDB deposits. You (and all intrested persons) will get access to 3ftt diffraction images next week. Best regards, Maks Chruszcz I do not know if it will be posted on CCP4BB. I have problem with authorization. ----- End forwarded message ----- -- =============================================================== * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===============================================================