From ccl@www.ccl.net Sun Aug 24 20:19:48 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id UAA15933; Sun, 24 Aug 1997 20:06:02 -0400 (EDT) Received: from jason05.u.washington.edu for mathomps@u.washington.edu by bedrock.ccl.net (8.8.6/950822.1) id UAA04595; Sun, 24 Aug 1997 20:06:00 -0400 (EDT) Received: from saul9.u.washington.edu (mathomps@saul9.u.washington.edu [140.142.82.7]) by jason05.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.05) with ESMTP id RAA02648 for ; Sun, 24 Aug 1997 17:06:01 -0700 Received: (from mathomps@localhost) by saul9.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.04) id RAA29000 for chemistry@ccl.net; Sun, 24 Aug 1997 17:05:59 -0700 (PDT) Date: Sun, 24 Aug 1997 17:05:59 -0700 (PDT) From: Mark Thompson Message-Id: <199708250005.RAA29000@saul9.u.washington.edu> To: chemistry@ccl.net Subject: Summary: software to add Hydrogens to proteins. Previously, I requested: > I need to find software that will add > hydrogens to proteins structures in > PDB format. It must run on a PC (win95 or NT). Here is a brief summary of the responses I received. I downloaded MSI's WebLab viewer (option B, below) and really like it. I still have not tried the other options. Thanks again to all who responded. Your suggestions were very helpful. Mark Thompson A). Rick Ornstein had a program called Network. It worked on Biosym car files; so maybe you could do a translation. I don't know if it is still maintained by his group. Also, it was written for UNIX but could probably be ported to NT. B) Try WebLab Viewer 2.0 - available free from MSI at http://www.msi.com/weblab/viewer/index.htm C) If you have a good Kekule structure available, then PCMODEL (Serena Software...812-3330823/Gilbert@indiana.edu) should be able to do it. D) Dear Mark, Babel (freeware) can add/subtract H atoms to several types of files, enclosed PDB files. I've not the exact address of it in mind while I'm writing but you may find a link to it in our software page at http://antas.agraria.uniss.it E) This is a very basic feature that probably isn't highlighted because just about every program can do it. Chem3D, Macromodel, and Hyperchem are among the three most-often-mentioned programs on this list, I think. All of them can do what you describe. For more information, see (in order): http://www.camsoft.com http://www.columbia.edu/cu/chemistry/mmod/mmod.html http://www.hyper.com F) Check out the Molecular Modelling Toolkit at http://starship.skyport.net/crew/hinsen/mmtk.html It has everything you need to addd hydrogens in reasonable (but not necessarily energy-minimized) positions to proteins. It's free and should run on Win95 and NT (but not DOS or Win 3.1 - it needs long file names), although I have tested it only on Unix systems. From ccl@www.ccl.net Sun Aug 24 22:32:22 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id VAA16637; Sun, 24 Aug 1997 21:36:31 -0400 (EDT) Received: from auric.chem.csiro.au for Dave.Winkler@molsci.csiro.au by bedrock.ccl.net (8.8.6/950822.1) id VAA05198; Sun, 24 Aug 1997 21:36:11 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA16729 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 25 Aug 1997 11:31:11 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Aug 1997 11:33:40 +1000 To: anchodd@postoffice.utas.edu.au, CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Structure-based Design at MGM EC-2 Dear Netters, <<<< I'm organizing a symposium on Structure-Based Design at the 2nd Electronic MGMS Conference in October. I would be happy to receive papers on any aspect of this topic for presentation and discvussion during the Symposium. I've attached an abridged version of the MGMS EC-2 announcement. Please accept my apologies for any duplication due to cross-posting. >>>> SECOND ELECTRONIC MOLECULAR GRAPHICS AND MODELLING CONFERENCE ************************************************************* The Second Electronic Molecular Graphics and Modelling Conference (MGM EC-2) will be held on the Internet and World Wide Web (http://www.vei.co.uk/mgmec2/) from Oct 6-17, 1997 and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure (Rod Hubbard); Membranes and Membrane Proteins (convener to be announced); Protein Folding (Jeffrey Skolnick); Modelling of In Vivo Activity (Ed Hodgkin); Knowledge-based Library Design (Mike Hann); Surface Science (Donald Brenner); Host-guest interactions (Jon Essex); Carbohydrates and Protein-Carbohydrate Interactions (Anne Imberty); Enzyme Mechanisms (Guy Grant); Conformational Sampling (convener to be announced); Nucleic Acids (convener to be announced); Quantum Chemistry (Tim Clark); Structure-based Design (David Winkler); Visualization (Art Olson); and Perspectives (Graham Richards). Authors can opt to have their presentation in the following categories: - non-permanent WWW presentation of a conference poster - non-permanent WWW presentation of a conference lecture - refereed WWW presentation which will be considered for print publication as a full paper in the Journal of Molecular Graphics - refereed WWW presentation which will be considered for permanent electronic publication in the Internet Journal of Chemistry (IJC), http://www.ijc.com/ Presentations of papers or posters must be prepared in Hypertext Markup Language (HTML) with figures in GIF or other Web-compatible formats so that participants can view the papers via the World Wide Web (The presentations may also include enhancements such as 3D structures, VRML, Java, RealAudio, Quicktime movies etc.) Powerpoint presentations can be used for the presentation of conference lectures. Aid and consultation is provided to participants who may address their queries to the conference hot-line at mgmnorg@vei.co.uk. Further details will be given in the authors' guide accessible via http://www.vei.co.uk/mgmec2/. During the conference interaction, presentations and discussions will take place via the Internet using a Java-based virtual conference centre, WWW-based discussion forums and an electronic mailing list. Before the conference, a timetable for lectures and discussion sessions for each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. DEADLINES AND DATES 1) DO NOW - The Molecular Graphics & Modelling & Graphics Network (MGMN) mailing list Conference-related news and announcements will be posted regularly to the MGMN mailing list (mgmn@vei.co.uk). If you are receiving this message from the mgmn list you are already subscribed. If you wish to subscribe to the MGMN list send the following one line message to mgmn-request@vei.co.uk: subscribe mgmn@vei.co.uk your_email@address To unsubscribe send the following message: unsubscribe mgmn@vei.co.uk your_email@address 2) Registration If you intend to participate in MGM EC-2 please use the special registration form accessible via http://www.vei.co.uk/mgmec2/. The electronic registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is Sept 1. Email your abstract directly to mgmec2abstracts@vei.co.uk. Fuller details of the scope of each section is given in the authors' guide accessible via http://www.vei.co.uk/mgmec2/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent poster or lecture, refereed as letter, refereed as full paper) you wish. If you are unsure as to which section your abstract is suitable for, please e-mail a possible section convener or Barry Hardy (barry@vei.co.uk). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is Sept 15. You must deposit your text and graphics files at the conference ftp site following the instructions available at http://www.vei.co.uk/mgmec2/. Any general e-mails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, etc) should be sent to: mgmnorg@vei.co.uk Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Division of Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC, http://www.csiro.au Clayton 3169, Australia http://www.molsci.csiro.au