Hi Anita A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you should upgrade to the latest version from the York website.
Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Anita Lewit-Bentley > Sent: 23 February 2009 15:31 > To: CCP4BB@JISCMAIL.AC.UK > Subject: TLS refinement in Refmac gets stuck > > Dear ccp4 folks, > > I am refining a structure in several crystal forms, with several molecules > in the asymmetric unit. The structure is rather flexible, so I am using > TLS refinement, having first submitted the coordinates to the TLSMD server > (http://skuld.bmsc.washington.edu/~tlsmd/ > <http://skuld.bmsc.washington.edu/~tlsmd/jobs/TLSMD7413_IBXkmSis/ANALYSIS/ > index.html> ). > > The TLS refinement worked OK with REFMAC 5.2.0019 (CCP4 6.0.2) for 3 > molecules in the asu, but not for crystal forms with 6 molecules/asu (it > just got hung). > > For the latter crystal forms I have switched to CCP4 6.1.0 with REFMAC > 5.5.0066, where it worked fine for two crystals - and now plays up for the > third crystal! > > It is not exactly crashing, so I don't know what is going on. This is the > last part of the logfile: > > "Problem > xyz 1230 5.6147661 -5.1691742 2.8234024 - > 1.55429840E-02 9.35771316E-02 0.17803398 0.23723726 -0.13626081 > 5.39243035E-02 -0.14011805 -1.55429840E-02 0.11864197 0.40574944 > 0.71992165 0.57164854 -0.39361250 > ************************************************************************** > * > * Information from CCP4Interface script > ************************************************************************** > * > Writing final coordinates (XYZOUT) to > /Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.pdb > ************************************************************************** > * > > ************************************************************************** > * > * Information from CCP4Interface script > ************************************************************************** > * > Writing final phases (HKLOUT) to > /Users/anita/work/Integ/SOLEIL_09_08/3M_Se_TLS_refmac1.mtz > ************************************************************************** > * > > ************************************************************************** > * > * Information from CCP4Interface script > ************************************************************************** > * > Writing final TLS (TLSOUT) to > /Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.tls > ************************************************************************** > * > " > Unfortunately, there are NO files written out! There is no real error > message either, the CCP4i interface says the job has finished normally. > > I have already tried to vary the number of TLS fragments, with no better > result. The older Refmac just gets hung.... > > Any help will be appreciated! > > Thanks, > > Anita > > > Anita Lewit-Bentley > > Unité d'Immunologie Structurale > CNRS URA 2185 > Département de Biologie Structurale & Chimie > Institut Pasteur > 25 rue du Dr. Roux > 75724 Paris cedex 15 > FRANCE > > Tel: 33- (0)1 45 68 88 95 > FAX: 33-(0)1 40 61 30 74 > email: ale...@pasteur.fr > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
