From geoff at compbio.dundee.ac.uk Fri Oct 7 14:29:59 2005 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Fri Oct 7 14:30:13 2005 Subject: [Discuss] test Message-ID: Test message to this list. Geoff. ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk From lepore at brandeis.edu Fri Oct 7 14:44:35 2005 From: lepore at brandeis.edu (Bryan W. Lepore) Date: Fri Oct 7 14:44:38 2005 Subject: [Discuss] poststamp parameters Message-ID: aha -it seems i should use this list instead of discuss@www.compbio.dundee.ac.uk. thanks a lot for checking into it Geoff. btw, the website says to use the latter... this seems wise. i want to align 83 structures in stamp, so i reset MAX_SEQ_LENGTH default so that stamp creates the alignment (e.g. my_stamp_scan.83 ). the problem is that poststamp segfaults and writes a my_stamp_scan.83.post file without a terminating asterisk (*). i figure recompiling will not fix it because poststamp.c has MAX_SEQ_LENGTH set to 10000 actually - are there some variables i should take note of? i also notice that section 4 of the manual does not cover poststamp. is MAX_SEQ_LENGTH the spacing of the longest aligned protein sequence? is there a way to get some debug info from poststamp? -bryan From geoff at compbio.dundee.ac.uk Fri Oct 7 14:54:06 2005 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Fri Oct 7 14:54:11 2005 Subject: [Discuss] poststamp parameters In-Reply-To: References: Message-ID: On Fri, 7 Oct 2005, Bryan W. Lepore wrote: > aha -it seems i should use this list instead of > discuss@www.compbio.dundee.ac.uk. thanks a lot for checking into it Geoff. > btw, the website says to use the latter... this seems wise. Bryan, I'm glad you got it to work. Can you tell me the page where it says to use discuss@www.compbio.dundee.ac.uk? That's an error and I need to fix it. Many thanks. > i want to align 83 structures in stamp, so i reset MAX_SEQ_LENGTH default so > that stamp creates the alignment (e.g. my_stamp_scan.83 ). the problem is that > poststamp segfaults and writes a my_stamp_scan.83.post file without a > terminating asterisk (*). > > i figure recompiling will not fix it because poststamp.c has MAX_SEQ_LENGTH set > to 10000 actually - are there some variables i should take note of? i also > notice that section 4 of the manual does not cover poststamp. > > is MAX_SEQ_LENGTH the spacing of the longest aligned protein sequence? is there > a way to get some debug info from poststamp? Which version of STAMP are you using and on which operating system? Thanks, Geoff. ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk From lepore at brandeis.edu Fri Oct 7 15:08:39 2005 From: lepore at brandeis.edu (Bryan W. Lepore) Date: Fri Oct 7 15:08:44 2005 Subject: [Discuss] poststamp parameters In-Reply-To: References: Message-ID: On Fri, 7 Oct 2005, Geoff Barton wrote: > Can you tell me the page where it says to use > discuss@www.compbio.dundee.ac.uk? http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > That's an error and I need to fix it. i figured it might be an effective way to avoid spam robots - but perhaps something different than www... i dunno... > Which version of STAMP are you using and on which operating system? Linux kernel release 2.4.21-32.0.1.ELsmp, STAMP version 4.2, it says: Last Modified: 25 March 1999 -bryan From geoff at compbio.dundee.ac.uk Fri Oct 7 15:14:42 2005 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Fri Oct 7 15:14:47 2005 Subject: [Discuss] poststamp parameters In-Reply-To: References: Message-ID: On Fri, 7 Oct 2005, Bryan W. Lepore wrote: > On Fri, 7 Oct 2005, Geoff Barton wrote: >> Can you tell me the page where it says to use >> discuss@www.compbio.dundee.ac.uk? > > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss Ah, I see. That is an error in mailman software. I'll report it. The list name is correct on our main web pages: http://www.compbio.dundee.ac.uk/Contact/Mailing_lists/mailing_lists.html > i figured it might be an effective way to avoid spam robots - but perhaps > something different than www... i dunno... Nothing that clever I am afraid. At least I don't think so... >> Which version of STAMP are you using and on which operating system? > > Linux kernel release 2.4.21-32.0.1.ELsmp, STAMP version 4.2, it says: Last > Modified: 25 March 1999 I'll email you a link to the very latest version. This may or may not fix your problem. Geoff. From lepore at brandeis.edu Fri Oct 7 18:10:50 2005 From: lepore at brandeis.edu (Bryan W. Lepore) Date: Fri Oct 7 18:11:00 2005 Subject: [Discuss] avestruc limits Message-ID: is there a limit on the number of proteins that avestruc can average together in a single pass? -bryan From lepore at brandeis.edu Sat Oct 8 21:01:36 2005 From: lepore at brandeis.edu (Bryan W. Lepore) Date: Sat Oct 8 21:03:25 2005 Subject: [Discuss] avestruc and missing atoms Message-ID: i am getting the "error: missing N atoms" (or CB atoms.. so far) message from avestruc with the -polyA option. i figure the pdb file lacks these just like it says, and i have to go add them back with emacs or somesuch. the C-alpha trace is fine. is there any other way to get avestruc -polyA to work around the missing atoms that does not involve editing pdb files? using the cleaned or poststamp files does not do it. of course omitting the pdb file works but there's always another one. -bryan From tom at compbio.dundee.ac.uk Mon Oct 10 11:35:47 2005 From: tom at compbio.dundee.ac.uk (Tom Walsh) Date: Mon Oct 10 10:38:48 2005 Subject: [Discuss] avestruc limits In-Reply-To: References: Message-ID: <434A4403.8080307@compbio.dundee.ac.uk> Bryan W. Lepore wrote: >is there a limit on the number of proteins that avestruc can average together in >a single pass? > There's no hard-coded limit on the number of structures. Tom