From n.keep@mail.cryst.bbk.ac.uk Wed Dec 7 11:57:53 2005 Date: Wed, 12 Oct 2005 17:56:05 +0100 From: Nicholas Keep To: ccp4@ccp4.ac.uk, Claire Naylor , Dr Nicholas Keep Subject: [ccp4]: [Fwd: Watertidy] Dear CCP4, See below for a bug report from Claire Naylor. I wish you well with this as it is a version 5 library problem in that ccp4_4.2.2 runs fine. A diff on the two watertidy.f src files shows nothing that I can see that has changed which would supress the printing of the protein coordinates and the previously assigned water shells which is a desired event. Best wishes Nick (Claire use 'ccp4_4.2.2' will work to run the ccp4_5/6 ccp4i watertidy job as the scripts were in ccp4_4.2.2 just no reference to them in the program lists). -------- Original Message -------- Subject: Watertidy Date: Wed, 12 Oct 2005 15:03:21 +0100 From: Claire Naylor To: Nicholas,Herbert Keep Hi Nick, I think there may be a problem with watertidy in ccp4i. If you run the program on default settings then the only output pdb file you get is a list of (probably? its not clear) junk waters, with the input chain id. I'm not familiar with the program but the documentation says you should get an output file with bad waters removed and the remaining waters relabelled to clearly link them with protein chains. Incidentally Kaj Sternberg reported this on ccp4bb on (I checked!) 22nd Sept at the end of a mail asking about the distang warning message that appears at the start of the program. Eleanor replied explaining about the warning, and noted in passing that 'you should be getting a file with waters linked to protein chains' but not explaining what might have happened in this case! The problem appears to date backsome distance, as running in ccp4_5.0.3 generates the same output, which makes me wonder if I'm doing the wrong thing on input? thanks claire ___________________________________________________________________________ Claire Naylor Dept of Crystallography, Birkbeck College, e-mail: c.naylor@mail.cryst.bbk.ac.uk Malet Street, tel: 0171-631-6835 LONDON, WC1E 7HX fax: 0171-631-6803 ___________________________________________________________________________ -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G59 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door