From Ben.Lewis at fmc.sa.gov.au Wed Dec 1 08:31:06 2004 From: Ben.Lewis at fmc.sa.gov.au (Lewis, Ben (FMC)) Date: Tue Nov 30 22:04:10 2004 Subject: [Jpred-list] Introduction... Message-ID: Hi all on the Jpred mailing list... I have just begun molecular modelling and look forward to utilizing jpred to optimize my alignments. Kind regards, Benjamin Lewis BSc (Hons) MRACI Chartered Chemist- Research Associate/PhD student Department of Clinical Pharmacology, Level 6, Flinders Medical Centre, Flinders University School of Medicine, Bedford Park, South Australia 5042, Australia. T +61 8 82044795 F +61 8 82045114 E ben.lewis@fmc.sa.gov.au W www.flinders.sa.gov.au CAUTION: The information contained in this e-mail is confidential and may be legally privileged. If the reader of this message is not the intended recipient you are hereby notified that any use, distribution, or reproduction of this message is prohibited. If you have received this message in error please forward this message to the return address and delete all copies of this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: /mailman/public/attachments/20041201/d519dffd/attachment.htm From Ben.Lewis at fmc.sa.gov.au Fri Dec 3 12:10:55 2004 From: Ben.Lewis at fmc.sa.gov.au (Lewis, Ben (FMC)) Date: Fri Dec 3 01:43:52 2004 Subject: [Jpred-list] RE: Jpred job jp_2743046 failed Message-ID: Thanks Jon. Whilst I have you here, I was wondering if I should actually be using Jpred for my entire sequence... You see I have a protein sequence that has 30% identity with three other proteins (all from different sub-families) for which crystal data has been obtained. Within the entire family of enzymes little structural differences are observed for those that have already been crystallised. My main problem being that the protein I am trying to model is not from one of the sub-families with crystallised isoforms. Should I only use Jpred structural predictions for those areas of the primary sequence that are not homologous to the model templates..? Regards, Benjamin Lewis BSc (Hons) MRACI Research Associate/PhD Student Department of Clinical Pharmacology, Level 6, Flinders Medical Centre, Flinders University School of Medicine, Bedford Park, South Australia 5042, Australia. T +61 8 82044795 F +61 8 82045114 E ben.lewis@fmc.sa.gov.au W www.flinders.sa.gov.au -------------------------------------------------------------------- -------------------------------------------------------------------- CAUTION: The information contained in this e-mail is confidential and may be legally privileged. If the reader of this message is not the intended recipient you are hereby notified that any use, distribution, or reproduction of this message is prohibited. If you have received this message in error please forward this message to the return address and delete all copies of this message. Thank You. --------------------------------------------------------------------- --------------------------------------------------------------------- -----Original Message----- From: Jonathan Barber [mailto:jon@compbio.dundee.ac.uk] Sent: Thursday, 2 December 2004 11:11 PM To: ben.lewis@fmc.sa.gov.au Subject: Re: Jpred job jp_2743046 failed On Thu, Dec 02, 2004 at 06:48:40AM +0000, www-jpred@compbio.dundee.ac.uk wrote: > For some reason your job did not complete successfully. The > administrator has been copied into this email and will investigate > whether there is a problem with the server. > > You may check the log at: > http://www.compbio.dundee.ac.uk/~www-jpred/cgi-bin/chklog?jp_2743046 Yes, the reason it isn't working is because you seem to be submitting the prediction from Jpred to Jpred. This probably won't work as the prediction can't really be considered as a protein sequence, even though it consists of characters that could be interpreted as amino acids. -- Jon From geoff at compbio.dundee.ac.uk Wed Dec 15 14:27:03 2004 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Wed Dec 15 14:27:10 2004 Subject: [Jpred-list] mailing list move Message-ID: Dear jpred-list, Warning. This mailing list and the will be unavailable for a few hours today while the list is migrated to a new server. Please don't try to post to this list until you see a message to say it is OK. With thanks, Geoff ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 345860/345843 (Fax:345764) www.compbio.dundee.ac.uk