From chemistry-request@server.ccl.net Mon Sep 30 06:17:25 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8UAHPd11727 for ; Mon, 30 Sep 2002 06:17:25 -0400 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.36 #3) id 17vxX1-0000xk-04; Mon, 30 Sep 2002 11:12:03 +0100 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id TZ104KJS; Mon, 30 Sep 2002 11:12:16 +0100 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Mon, 30 Sep 2002 11:12:16 +0100 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE14A6@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'Mark Thompson'" , chemistry@ccl.net Subject: RE: Free software to generate 3D protein structure from sequence? Date: Mon, 30 Sep 2002 11:12:15 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean For homology modelling, there is Deep View (which is used in combo with the SwissModel server): http://www.expasy.ch/spdbv/ or for a more advanced approach (i.e. lots more user control) there's MODELLER: http://tatiana.rockefeller.edu/modeller/ They both have fairly active and helpful mailing lists too. Mike -----Original Message----- From: Mark Thompson [mailto:mark@planaria-software.com] Sent: 29 September 2002 17:06 To: chemistry@ccl.net Subject: CCL:Free software to generate 3D protein structure from sequence? I'd like to find out about free software for generating 3D protein structures from sequence data, possibly using existing crystal structures of homologous proteins for refinement. Thanks in advance. I'll summarize what I find out. Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Sun Sep 29 20:29:30 2002 Received: from medusa.wo.utoledo.edu (IDENT:WQE4192CdguL4Rkq3JAI6NnKKA/K5z5z@[131.183.69.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8U0TUd26488 for ; Sun, 29 Sep 2002 20:29:30 -0400 Received: from there (IDENT:Bl6VlMK3R6fsC0ZN19zEGPvJ0IztvGNp@localhost.localdomain [127.0.0.1]) by medusa.wo.utoledo.edu (8.11.6/8.11.6) with SMTP id g8U0WU513507 for ; Sun, 29 Sep 2002 20:32:30 -0400 Message-Id: <200209300032.g8U0WU513507@medusa.wo.utoledo.edu> Content-Type: text/plain; charset="iso-8859-1" From: Venkataraman Kabaleeswaran Reply-To: vkabale@uoft02.utoledo.edu Organization: univ of toledo To: chemistry@ccl.net Subject: - homology model building Date: Sun, 29 Sep 2002 20:32:29 -0400 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit try JACKAL computer program , that is free for academic or there or some servers that can do for you or Modeller. check this web site http://trantor.bioc.columbia.edu/~xiang/jackal/ it is free and easy to use. cheers venkatarman Kabaleeswaran From chemistry-request@server.ccl.net Sun Sep 29 20:31:54 2002 Received: from medusa.wo.utoledo.edu (IDENT:AZ4FV44q6QUj2b3iPvW/F0YA7gn5asUV@[131.183.69.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8U0Vrd26568 for ; Sun, 29 Sep 2002 20:31:53 -0400 Received: from there (IDENT:3BZd37bYQhZ0PRg+YPgvliSNWAw0Q88C@localhost.localdomain [127.0.0.1]) by medusa.wo.utoledo.edu (8.11.6/8.11.6) with SMTP id g8U0Yr513517; Sun, 29 Sep 2002 20:34:53 -0400 Message-Id: <200209300034.g8U0Yr513517@medusa.wo.utoledo.edu> Content-Type: text/plain; charset="iso-8859-1" From: Venkataraman Kabaleeswaran Reply-To: vkabale@uoft02.utoledo.edu Organization: univ of toledo To: chemistry@ccl.net Subject: homology model building Date: Sun, 29 Sep 2002 20:34:53 -0400 X-Mailer: KMail [version 1.3.1] Cc: Mark Thompson MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Try JACKAL - a computer program , that is free for academic check this web site http://trantor.bioc.columbia.edu/~xiang/jackal/ it is free and easy to use. cheers venkatarman Kabaleeswaran >>>>>>>>>>>>>>>>.>>>>>>>>>> I'd like to find out about free software for generating 3D protein structures from sequence data, possibly using existing crystal structures of homologous proteins for refinement. Thanks in advance. I'll summarize what I find out. Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= From chemistry-request@server.ccl.net Mon Sep 30 00:09:19 2002 Received: from web20422.mail.yahoo.com ([66.163.169.98]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8U49Id01609 for ; Mon, 30 Sep 2002 00:09:19 -0400 Message-ID: <20020930040918.50395.qmail@web20422.mail.yahoo.com> Received: from [202.185.66.42] by web20410.mail.yahoo.com via HTTP; Sun, 29 Sep 2002 21:09:18 PDT Date: Sun, 29 Sep 2002 21:09:18 -0700 (PDT) From: Juraina Jamil Subject: AutoDock compiling To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I've been having some problems recompiling autodock after making some value changes in a couple of its files required for compilation. For everyone's information, I'm recompiling it on Redhat 6.2. At first, I only changed the MAX_TORS value in constants.h file and managed to recompile autodock despite some warnings. But I could not run autodock, it asked me to change the LINE_LEN value since I changed the MAX_TORS. And so I increased the LINE_LEN value and tried recompiling again but it gave me these errors: > ar r libad.a call_gs.o cmdmode.o readmap.o > readPDBQ.o eval.o getrms.o getInitialState.o > initautodock.o openfile.o writeMolAsPDBQ.o writePDBQ.o > writePDBQState.o prTorConList.o simanneal.o success.o > summarizegrids.o > ranlib libad.a > echo . ' on '`date`', using '`hostname` >> > LATEST_MAKE > echo 'Flags: 'gcc -O3 -DNOSQRT -L. -lad -lm >> > LATEST_MAKE > gcc -O3 -DNOSQRT -o autodock3 main.o -L. -lad -lm > ./libad.a(readPDBQ.o): In function `readPDBQ(char *, > char *, int, int *, float (*)[2], float *, char *, int > *, char (*)[4], char *, char (*)[127], int, char *, > int *, int *, float *, float *, int *, int *, int > (*)[2047], float (*)[2], int *, int *, int (*)[1], > long, tms, char *, int *)': > readPDBQ.o(.text+0x6f1): undefined reference to > `mkTorTree(int *, char (*)[199], int, int (*)[2047], > int *, char *, char (*)[4], char *, int *, int *, > float *, float *, int *)' > readPDBQ.o(.text+0x743): undefined reference to > `nonbonds(float (*)[2], int (*)[2047], int, int *, > int, char (*)[199], int *, int, int *)' > collect2: ld returned 1 exit status > make: *** [autodock3] Error 1 Not being a computer person, I've no ides what the above means. Can anyone help me out, pls. Frustrated and desperate, Juraina __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com From chemistry-request@server.ccl.net Mon Sep 30 15:35:11 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g8UJZBm22670 for chemistry@server.ccl.net; Mon, 30 Sep 2002 15:35:11 -0400 Received: from 150.214.196.182 ( [150.214.196.182]) as user smelchor@goliat.ugr.es by webmail.ugr.es with HTTP; Mon, 30 Sep 2002 18:12:38 +0200 Message-ID: <1033402358.3d9877f6f1c9d@webmail.ugr.es> Date: Mon, 30 Sep 2002 18:12:38 +0200 From: smelchor@ugr.es To: chemistry@ccl.net Subject: Carbon Nanotubes Coordinates Dear Zheng, I am just finishing my PhD Thesis about nanotubes with defects "Graphitic Nanotubes with Disclinations: Electronic Structure, topology and conductivity", and I have developed a program that generates the coordinates of a nanotube, just introducing the indices and the length. Unfortunately, the code is not finished, and is only in Beta stage. Nevertheless, you can tell me which indices of tubes you are interested in (and length), and I can give you the coordinates in *.mol format (readable with Hyperchem) You can find mor information from our group in www.ugr.es/local/gmdm Sinderely, Santiago Melchor. smelchor@ugr.es > > A friend of mine is interested in examining how a carbon nanotube interacts > with other molecules. There have been some theoretical studies regarding > the structures of some carbon nanotubes and I am wondering whether anyone > would be kind to share the coordinates of a nanotube model. Thanks. > > Yajun