From chemistry-request@server.ccl.net Mon Nov 6 02:36:29 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA30377 for ; Mon, 6 Nov 2000 02:36:28 -0500 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id IAA00391; Mon, 6 Nov 2000 08:36:20 +0100 (MET) Message-Id: <4.3.2.7.0.20001106083926.00a9e100@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Mon, 06 Nov 2000 08:44:44 +0100 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Computation of a vdW surface area Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues; Attached to the end of this note is a MOPAC internal coordinates file for the molecule endosulfan. If anyone can use this MOPAC strufture to calculate the van der Waals (not solvent accessible) surface area of endosulfan _as is_ (i.e. without minimisation or other modification), I'd appreciate hearing from you. I will need to know the value of your calculated vdW surface area (A^2) and the identify of the software you used to compute it. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch endosulfan C .0000000 0 .000000 0 .000000 0 0 0 0 -.1183 C 1.3640004 1 .000000 0 .000000 0 1 0 0 -.1183 C 1.5302830 1 107.681177 1 .000000 0 2 1 0 .0015 C 1.5590279 1 106.268367 1 -69.310489 1 3 2 1 -.1340 C 1.5893475 1 99.373109 1 34.896666 1 3 2 1 -.0118 C 1.5512879 1 103.771872 1 66.591781 1 4 3 2 -.1340 C 1.5229597 1 111.424881 1 -59.777500 1 4 3 2 .0042 C 1.5590308 1 103.771727 1 .000028 1 6 4 3 .0015 C 1.5229603 1 116.690939 1 -122.967962 1 6 4 3 .0042 O 1.4058961 1 110.156396 1 -171.583524 1 7 4 3 -.5612 S 1.6938299 1 120.130298 1 -95.480740 1 10 7 4 1.5538 O 1.6938262 1 96.573679 1 65.812685 1 11 10 7 -.5612 Cl 1.6596609 1 128.659068 1 -179.936635 1 1 2 3 .0818 Cl 1.6596606 1 123.659467 1 -179.942079 1 2 3 1 .0818 Cl 1.7182783 1 116.642821 1 160.320025 1 3 2 1 -.0019 H 1.1253651 1 109.025692 1 -178.067054 1 4 3 2 .1400 H 1.1253652 1 108.384673 1 115.794975 1 6 4 3 .1400 Cl 1.7182766 1 115.476151 1 162.375562 1 8 6 4 -.0019 H 1.1269771 1 109.439701 1 -56.473152 1 7 4 3 .1217 H 1.1249895 1 111.744821 1 64.497415 1 7 4 3 .1108 O 1.4389259 1 100.727099 1 -36.457835 1 11 10 7 -.7972 H 1.1269769 1 109.440370 1 175.387387 1 9 6 4 .1217 H 1.1249914 1 111.744421 1 54.416706 1 9 6 4 .1108 Cl 1.7442039 1 114.193008 1 -169.848191 1 5 3 2 -.0208 Cl 1.7457317 1 113.222061 1 64.629345 1 5 3 2 -.0132 From chemistry-request@server.ccl.net Sun Nov 5 23:09:33 2000 Received: from mail.sunesis-pharma.com (mail.sunesis-pharma.com [209.182.138.82]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA29629 for ; Sun, 5 Nov 2000 23:09:32 -0500 Received: from sunesis-pharma.com ([64.165.121.186]) by mail.sunesis-pharma.com (Netscape Messaging Server 4.15) with ESMTP id G3L5BT00.N0L; Sun, 5 Nov 2000 20:19:05 -0800 Message-ID: <3A0631C1.AC7B617@sunesis-pharma.com> Date: Sun, 05 Nov 2000 20:21:21 -0800 From: "Warren DeLano" To: chemistry@ccl.net, ccp4bb@dl.ac.uk Subject: PyMOL 0.41 Windows Binaries Released PyMOL is a molecular graphics program which uses Python as its scripting language. It is still under development and is not yet ready for usage by novices. However, experienced molecular graphics users and developers who know Python may find it valuable in its present form. I have compiled a Win32 installable binary and placed it on the SourceForge web site ( http://pymol.sourceforge.net ). Unix users can compile the source from the CVS repository. This is an early release, so please set your expectations low. The GUI is very limited, and you will almost certainly encounter problems. What PyMOL currently provides is real-time and scriptable molecular graphics capabilities on very low cost hardware. In fact, I have posted a recipe on the web site for a $1000 Athlon-based PC system which will outperfom an SGI Octane costing over 30X as much. PyMOL itself is free, open-source, and 100% unrestricted. You can use PyMOL for some of the same tasks you currently perform with non-free programs such as Midas, Insight II, Grasp, Molscript, O, and Macromodel (no minimization yet). You can also build in-house systems or new products around PyMOL without paying anyone a dime or having to disclose your modifications (as under GPL). Unfortunately, documentation on how to do some of these tasks is currently non-existent. My apologies, but that is the nature of free/unfinished software. The project is hosted on SourceForge. Developers, testers, and documenters are needed. Development will progress slowly without some extra help! NOTE: Under windows you will need: (1) A fast accelerated 3D graphics card with OpenGL (REQUIRED). (2) Python 1.52 installed ( http://www.python.org ) (3) A three-button mouse. PyMOL's capabilties are numerous. Highlights include: - Fast real-time 3D graphics with OpenGL. - A flexible atom selection language derived from X-PLOR. - Seven molecular representations including surfaces. - Animation of 1000+ states (trajectories, etc). - A built-in ray-tracer for photorealistic images and movies. - Display of electron density from XPLOR map files. - Molecular editing capabilities. - 100% scriptable. and more.... http://www.pymol.org Warren L. DeLano, Ph.D. DeLano Scientific mailto:warren@delanoscientific.com or mailto:warren@sunesis-pharma.com From chemistry-request@server.ccl.net Mon Nov 6 01:39:56 2000 Received: from donjuan.stud.chemie.tu-muenchen.de (root@donjuan.stud.chemie.tu-muenchen.de [129.187.245.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA30163 for ; Mon, 6 Nov 2000 01:39:55 -0500 Received: from ch.tum.de (dialk003.ppp.lrz-muenchen.de [129.187.42.3]) by donjuan.stud.chemie.tu-muenchen.de (8.9.3/8.9.3/Debian/GNU) with ESMTP id HAA03418 for ; Mon, 6 Nov 2000 07:39:47 +0100 X-Authentication-Warning: donjuan.stud.chemie.tu-muenchen.de: Host dialk003.ppp.lrz-muenchen.de [129.187.42.3] claimed to be ch.tum.de Message-ID: <3A065254.4E0DAC18@ch.tum.de> Date: Mon, 06 Nov 2000 07:40:20 +0100 From: Peter Koenig X-Mailer: Mozilla 4.75 [en] (Windows NT 5.0; U) X-Accept-Language: de,en,en-US MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: hello References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, AFAIK there is no way of writing the answer to this question in a closed formula. However I have a citation of G. P´olya who apparently wrote an article on this topic: G. P´olya, Acta Mathematica, 68, 1937 Peter dido dido2 wrote: > > Can you tell me the formula for determination number of isomers according to > number of carbon atoms at alkanes?? > please From chemistry-request@server.ccl.net Mon Nov 6 02:29:49 2000 Received: from mail.inha.ac.kr (mail.inha.ac.kr [165.246.10.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA30326 for ; Mon, 6 Nov 2000 02:29:46 -0500 Received: from kim (77 [165.246.154.77]) by mail.inha.ac.kr with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id WASX74T2; Mon, 6 Nov 2000 16:27:22 +0900 Message-ID: <009c01c047c4$8828a0e0$4d9af6a5@inha.ac.kr> From: "Chan Kyung Kim" To: Subject: Scaling factor of MIDI!6D basis set Date: Mon, 6 Nov 2000 16:38:18 +0900 Dear Computational Chemists; I am looking for a scaling factor of MIDI!6D basis set. It is not listed in the J. Phys. 100, 16502 (1996) and cccbdb. Thanks in advance. Sincerely, Chan =============================================================================== Prof.Chan Kyung Kim (Tel) +82-32-860-7684 Department of Chemistry (Fax) +82-32-867-5604 or +82-32-873-9333 Inha University (e-mail) kckyung@inha.ac.kr Inchon, 402-751, Korea (homepage) http://dragon.inha.ac.kr/~kckyung(Korean) =============================================================================== From chemistry-request@server.ccl.net Mon Nov 6 11:22:44 2000 Received: from hera.lion-ag.de ([217.5.141.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA00492 for ; Mon, 6 Nov 2000 11:22:43 -0500 Received: from lionbioscience.com (lionsp124.lion-ag.de [172.16.10.46]) by hera.lion-ag.de (8.9.3/8.9.3) with ESMTP id RAA19250 for ; Mon, 6 Nov 2000 17:25:05 +0100 Message-ID: <3A06DAC0.234FF7F1@lionbioscience.com> Date: Mon, 06 Nov 2000 17:22:25 +0100 From: Lutz Ehrlich Reply-To: lutz.ehrlich@lionbioscience.com Organization: LION bioscience AG To: chemistry@ccl.net Subject: RevCompChem bibtex style? Dear colleagues, could somebody point me to a BIBTEX style file that complies to the reference style for 'Reviews in Computational Chemistry' ? If you know of a solution (even a half-baked one) I would appreciate if you emailed me personally. Best regards, Lutz Ehrlich Ehrlich Lutz tel. work: +49-6221-4038371 LION bioscience AG lutz.ehrlich@lionbioscience.com Project Manager From chemistry-request@server.ccl.net Mon Nov 6 13:44:08 2000 Received: from newmail.DKFZ-Heidelberg.DE (newmail.inet.dkfz-heidelberg.de [193.174.53.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA01481 for ; Mon, 6 Nov 2000 13:44:06 -0500 Received: from DKFZ-heidelberg.de (vishnu.inet.dkfz-heidelberg.de [193.174.62.115]) by newmail.DKFZ-Heidelberg.DE (8.9.3/8.9.3/DKFZ-8.9.3) with ESMTP id TAA12461 for ; Mon, 6 Nov 2000 19:41:51 +0100 (MET) Message-ID: <3A06FB63.C16A0CAA@DKFZ-heidelberg.de> Date: Mon, 06 Nov 2000 19:41:39 +0100 From: Chaitanya Athale Organization: DKFZ-Heidelberg X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chem computing Subject: Polymerization Simulation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Everbody, 1) I am attempting to make a model of a Polymerizing Protein, which builds micron-long filaments. 2) The model is to be coarse grained model (no atomic structure available) of this, using concepts of Statstical Physics, 3) As an output I am interested in measuring the Conformation of entire chains (lenght etc.). If anybody knows of such an implementation, maybe from other applications like organic polymers etc, please do let me know. Cheers, Chaitanya. -- Mr. Chaitanya Athale Heidelberg. Email: c.athale@DKFZ-heidelberg.de From chemistry-request@server.ccl.net Mon Nov 6 19:38:12 2000 Received: from mail2.panix.com (mail2.panix.com [166.84.0.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA03154 for ; Mon, 6 Nov 2000 19:38:12 -0500 From: kynn@panix.com Received: from panix3.panix.com (panix3.panix.com [166.84.0.228]) by mail2.panix.com (Postfix) with ESMTP id B0A7A8ED1 for ; Mon, 6 Nov 2000 19:38:10 -0500 (EST) Received: (from kynn@localhost) by panix3.panix.com (8.8.8/8.7.1/PanixN1.0) id TAA06989; Mon, 6 Nov 2000 19:38:10 -0500 (EST) Date: Mon, 6 Nov 2000 19:38:10 -0500 (EST) Message-Id: <200011070038.TAA06989@panix3.panix.com> X-Authentication-Warning: panix3.panix.com: kynn set sender to kynn@panix.com using -f To: chemistry@ccl.net Subject: QUANTA: helix cartoon from CA-trace? Dear CCL: I like the "protein cartoons" that QUANTA produces (with secondary structure elements appearing like fetuccine and unstructured elements like spaghetti--maybe it should be called PASTA instead of QUANTA, but I digress). I know how to produce these cartoons (via QUANTA) using a full-atom PDB file for my coordinates data, but I can't figure out how to do it if the PDB contains only C-alpha coordinates (even when the PDB file has Helix records in it). In this case, QUANTA seems unable to recognize secondary structure elements, so it renders the whole protein as an unstructured (spaghetti) trace. I've heard that it is possible to coax QUANTA into producing the sort of cartoon I want even from a C-alpha-only PDB file. Can someone tell me how to do this? Thanks! Kevin From chemistry-request@server.ccl.net Mon Nov 6 15:21:11 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA01871 for ; Mon, 6 Nov 2000 15:21:10 -0500 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id VAA02040; Mon, 6 Nov 2000 21:20:45 +0100 X-Authentication-Warning: yogi.pc1.uni-duesseldorf.de: jochen set sender to jochen@pc1.uni-duesseldorf.de using -f Sender: jochen@pc1.uni-duesseldorf.de To: chemistry@ccl.net Subject: Re: CCL:RevCompChem bibtex style? References: <3A06DAC0.234FF7F1@lionbioscience.com> User-Agent: XEmacs/Gnus X-Face: -%Z4EZ6iY'4m:wiK:!v In-Reply-To: Lutz Ehrlich's message of "Mon, 06 Nov 2000 17:22:25 +0100" Date: 06 Nov 2000 21:20:45 +0100 Message-ID: Lines: 19 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit >>>>> Lutz Ehrlich writes: LE> could somebody point me to a BIBTEX style file that complies to LE> the reference style for 'Reviews in Computational Chemistry' ? If Have you searched CTAN? Looked at natbib? LE> you know of a solution (even a half-baked one) I would appreciate LE> if you emailed me personally. A halfbacked one: Use custom-bib to create it, it's pretty easy if you know what it is supposed to look like. Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 GnuPG key: 44BCCD8E 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195