Message

Axiom Discovery is pleased to announce the = release of=20 Molecule Viewer as a free software download. This release supplants previous versions of = the=20 software and includes fixes and several new features. =

Molecule Viewer is=20 a Microsoft Windows application that works in a similar way to the = Windows=20 Picture and Fax Viewer that is part of the Windows operating=20 system.

Molecule Viewer allows users to view = molecular=20 structures stored in a wide variety of file formats including Brookhaven = PDB,=20 Alchemy, MDL, Gaussian, MOPAC, etc by simply right-clicking on the file = in=20 Windows Explorer and selecting the "Preview" command.

Features include:

-=20 view structures in traditional renderings such as ball and stick=20

-=20 view proteins as ribbons, cartoons, barrels and tubes=20

-=20 view solvent accessible surfaces

-=20 view molecular orbitals and iso-density surfaces saved in Axiom = Discovery=20 workspace files

-=20 animation of normal modes

-=20 supports many common molecular=20 file formats including = PDB=20

-=20 print images direct to a printer

-=20 full control over how the image is rendered including background = colors=20 and gradients, projection, anti-aliasing, etc.

For = further=20 details and instructions on how = to=20 download the software please visit our web site at

www.axiomdiscovery.com

Regards,

Kam = Chana,Ph.D.

Axiom Discovery,=20 Inc.

------=_NextPart_000_0017_01C48EF1.B6560610-- From chemistry-request@ccl.net Tue Aug 31 17:43:28 2004 Received: from chemail.tamu.edu (Chennov3.tamu.edu [165.91.170.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7VMhQuu020101 for ; Tue, 31 Aug 2004 17:43:27 -0500 Received: from CHE l0y1935 [165.91.170.169] by chemail.tamu.edu with NetMail SMTP Agent $Revision: 3.22.1.13 $ on Novell NetWare; Tue, 31 Aug 2004 17:52:34 -0500 Message-ID: <007e01c48fad$3481c310$a9aa5ba5@CHE> From: "Liuming Yan" To: Subject: How to change the thresholds for plotting the bonds between atoms in GaussianView 3.0? Date: Tue, 31 Aug 2004 17:52:34 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_007B_01C48F83.4BA21E20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_007B_01C48F83.4BA21E20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I am using Gaussian 3.0 and find out that the default bond length for = some of the bonds is too short, therefore, some of the atom pairs are = not linked with a bond. When this happens, I have to connect these atom = pairs manually, Do you know how to increase the default bond length so = that these atom pairs will be connect automatically? thanks and I will summarize if needed Dr. Liuming Yan Department of Chemical Engineering Texas A & M University, 3122 TAMU College Station, TX 77843-3122 phone: (979)458-3532 ------=_NextPart_000_007B_01C48F83.4BA21E20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear=20 All,

I am using=20 Gaussian 3.0 and find out that the default bond length for some of the = bonds is=20 too short, therefore, some of the atom pairs are not linked with a = bond. =20 When this happens, I have to connect these atom pairs manually, Do you = know how=20 to increase the default bond length so that these atom pairs will be = connect=20 automatically?
thanks and I will summarize if = needed

Dr. Liuming Yan
Department of = Chemical=20 Engineering
Texas A & M University, 3122 TAMU
College = Station, =20 TX 77843-3122
phone: (979)458-3532

------=_NextPart_000_007B_01C48F83.4BA21E20-- From chemistry-request@ccl.net Tue Aug 31 15:31:45 2004 Received: from mailfe04.swip.net (mailfe04.swip.net [212.247.154.97]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7VKVguu010287 for ; Tue, 31 Aug 2004 15:31:43 -0500 X-T2-Posting-ID: 442u/WtJiSHUAn31jJObTujyZw7dsLBiHq866AtC57s= Received: from [83.176.42.191] (HELO avdemo.tiscalinet.ch) by mailfe04.swip.net (CommuniGate Pro SMTP 4.2b8) with ESMTP id 149142821 for chemistry{at}ccl.net; Tue, 31 Aug 2004 22:40:47 +0200 Message-Id: <5.0.2.1.0.20040831223747.02092a30{at}mail.tiscalinet.ch> X-Sender: barry.hardy{at}mail.tiscalinet.ch X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Tue, 31 Aug 2004 22:39:05 +0200 To: chemistry{at}ccl.net From: Barry Hardy Subject: CFP, Program & Submissions: Applications of Cheminformatics & Chemical Modelling in Drug Discovery Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_29760506==_.ALT" X-Spam-Status: No, hits=1.1 required=7.5 tests=HTML_FONTCOLOR_BLUE, HTML_MESSAGE,MAILER_VERSION autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_29760506==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The eCheminfo 2004 conference "Applications of Cheminformatics & Chemical Modelling in Drug Discovery" takes place 8-19 November 2004. (See http://echeminfo.com/ for further information and to register.) Further summary information on program and poster & paper submission follow here. Program The program for eCheminfo 2004 currently already involves over 60 seminars in the following session topic areas: Libraries, Virtual Screening, Docking, QSAR, Quality Control & Validation, Protein Modelling, Modelling of Membranes & Ion channels, QM/MM, Open Source, Grid Computing and Drug Design. Conference Brochure: http://conferences.metalayer.net/echeminfo/design/conference/dcechemininfoflyerregform.pdf Conference Program (with abstracts & bios): http://conferences.metalayer.net/echeminfo/design/conference/html/speakerinfoechem.htm Community & Conference Blog (news & views): http://barryhardy.blogs.com/cheminfostream/ Format This is a virtual conference so you can listen to the talks at any time > from any place using an Internet connection and phone; no special equipment is required. All conference seminars including audio are made available through http://echeminfo.com/ both during and after the conference. Conference registrants may exchange messages and contact information through the Web site. Conference discussions and question sessions will be held via phone conference and Web-based discussion-based facilities. Call for Posters All eCheminfo 2004 registrants are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted to Barry Hardy at echeminfo{at}douglasconnect.com by 30 September 2004. Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents. All accepted Posters in 2004 will be eligible for the eCheminfo 2004 Best Poster Awards. Publication Option All eCheminfo 2004 conference registrants are offered the option of submitting a paper for refereed publication in the Journal "Molecular Simulation". All accepted papers will be included in a special issue of Molecular Simulation devoted to the theme of eCheminfo 2004 "Applications of Cheminformatics & Chemical Modelling to Drug Discovery". The special issue will be co-edited by the Conference Chairs, David Lloyd (Trinity College), Brad Feuston (Merck) and Barry Hardy (Douglas Connect) and is scheduled for publication in April 2005. The final decision on approval for all papers will rest with Molecular Simulations's Chief Editor, Prof. Nick Quirke, Imperial College London. Submitted papers should follow the guidelines of the Molecular Simulation journal located at: http://www.tandf.co.uk/journals/titles/08927022.asp If you intend to submit a paper please notify Barry Hardy at echeminfo{at}douglasconnect.com and submit an abstract of ca. 300 words by 30 September 2004. best regards Barry Hardy Barry Hardy, PhD Douglas Connect, Switzerland www.douglasconnect.com +41 61 851 0170 (office) Email: barry.hardy{at}tiscalinet.ch --=====================_29760506==_.ALT Content-Type: text/html; charset="us-ascii"
The eCheminfo 2004 conference Applications of Cheminformatics & Chemical Modelling in Drug Discovery takes place 8-19 November 2004. (See http://echeminfo.com/ for further information and to register.) Further summary information on program and poster & paper submission follow here.

Program

The program for eCheminfo 2004 currently already involves over 60 seminars in the following session topic areas: Libraries, Virtual Screening, Docking, QSAR, Quality Control & Validation, Protein Modelling, Modelling of Membranes & Ion channels, QM/MM, Open Source, Grid Computing and Drug Design.

Conference Brochure: http://conferences.metalayer.net/echeminfo/design/conference/dcechemininfoflyerregform.pdf

Conference Program (with abstracts & bios): http://conferences.metalayer.net/echeminfo/design/conference/html/speakerinfoechem.htm

Community & Conference Blog (news & views):
http://barryhardy.blogs.com/cheminfostream/

Format

This is a virtual conference so you can listen to the talks at any time from any place using an Internet connection and phone; no special equipment is required. All conference seminars including audio are made available through http://echeminfo.com/ both during and after the conference. Conference registrants may exchange messages and contact information through the Web site. Conference discussions and question sessions will be held via phone conference and Web-based discussion-based facilities.

Call for Posters

All eCheminfo 2004 registrants are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted to Barry Hardy at echeminfo{at}douglasconnect.com by 30 September 2004.

Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents.

All accepted Posters in 2004 will be eligible for the eCheminfo 2004 Best Poster Awards.

Publication Option

All eCheminfo 2004 conference registrants are offered the option of submitting a paper for refereed publication in the Journal Molecular Simulation . All accepted papers will be included in a special issue of Molecular Simulation devoted to the theme of eCheminfo 2004 Applications of Cheminformatics & Chemical Modelling to Drug Discovery . The special issue will be co-edited by the Conference Chairs, David Lloyd (Trinity College), Brad Feuston (Merck) and Barry Hardy (Douglas Connect) and is scheduled for publication in April 2005. The final decision on approval for all papers will rest with Molecular Simulations s Chief Editor, Prof. Nick Quirke, Imperial College London.

Submitted papers should follow the guidelines of the Molecular Simulation journal located at:

http://www.tandf.co.uk/journals/titles/08927022.asp

If you intend to submit a paper please notify Barry Hardy at echeminfo{at}douglasconnect.com and submit an abstract of ca. 300 words by 30 September 2004.

best regards
Barry Hardy

Barry Hardy, PhD
Douglas Connect, Switzerland
www.douglasconnect.com
+41 61 851 0170 (office)
Email: barry.hardy{at}tiscalinet.ch
--=====================_29760506==_.ALT-- From chemistry-request@ccl.net Tue Aug 31 17:08:44 2004 Received: from web54005.mail.yahoo.com (web54005.mail.yahoo.com [206.190.36.229]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i7VM8guu016798 for ; Tue, 31 Aug 2004 17:08:42 -0500 Message-ID: <20040831212902.63741.qmail/at/web54005.mail.yahoo.com> Received: from [129.137.227.1] by web54005.mail.yahoo.com via HTTP; Tue, 31 Aug 2004 14:29:02 PDT Date: Tue, 31 Aug 2004 14:29:02 -0700 (PDT) From: muad dib Subject: CCL: RE: Freeware for molecular surface and surface normals To: CHEMISTRY/at/ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Yes, there is a very good open source program by the name of dms which can be found here: http://www.cgl.ucsf.edu/Overview/software.html#dms I found this program useful in computing surfaces for Dock5. Basically, it creates records (lines) for points on the Connoly surface at a user-specified density (points/(sqr A)) ~ David Rogers __________________________________ Do you Yahoo!? Yahoo! Mail Address AutoComplete - You start. We finish. http://promotions.yahoo.com/new_mail