From chemistry-request@server.ccl.net Wed Sep 4 01:24:07 2002 Received: from devonshire.cnchost.com ([207.155.248.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g845O7302635 for ; Wed, 4 Sep 2002 01:24:07 -0400 Received: from guillermo ([63.127.188.217]) by devonshire.cnchost.com id BAA06349; Wed, 4 Sep 2002 01:24:00 -0400 (EDT) [ConcentricHost SMTP Relay 1.14] Errors-To: Reply-To: From: "Guillermo A. Morales" To: "parthi.s" , Subject: RE: Image to molecular structure Date: Tue, 3 Sep 2002 22:20:52 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-reply-to: <200209030615.g836FUQ24949@jubilantbiosys.com> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 CLiDE from SimBioSys Inc. can do that. For more infocheck their website http://www.simbiosys.ca/clide/index.html Kekule from Oxford Molecular Group (now part of Accelrys Inc.) can do that too, but I believe now Kekule is discontinued and not longer available. I hope this helps. Best, Guillermo. ----- Dr. Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of parthi.s Sent: Monday, September 02, 2002 11:16 PM To: chemistry@ccl.net Subject: CCL:Image to molecular structure Dear CClers: Is there any program that can convert an image of a molecular structure (gif, jpeg) to molecular structure in some formats like mol2, smiles, car, xyz and so on. I am sure there would have been some attempt to scan the molecular structures from journals/patents and convert them in some formats. Any information in this line would be appreciated. I will summarise the responses. Thanks and Regards S. Parthiban Jubilant Biosys Ltd. (http://www.jubilantbiosys.com) #18, SJM Towers, 4th Floor Sheshadri Road, Gandhinagar Bangalore 560 009 INDIA Tel: 220 7301 to 220 7309 Fax: 220 7310 -= 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 Wed Sep 4 06:30:33 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g84AUX308991 for ; Wed, 4 Sep 2002 06:30:33 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H1W006F5T6K64@mailstudenti.unimi.it> for chemistry@ccl.net; Wed, 04 Sep 2002 12:30:21 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H1W00IGET6L04@smtp.unimi.it> for chemistry@ccl.net; Wed, 04 Sep 2002 12:30:22 +0200 (MEST) Date: Wed, 04 Sep 2002 12:37:05 +0200 From: Giulio Vistoli Subject: Announcing VEGA1.4.2 To: CCL Message-id: <000f01c253ff$03748910$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal Dear collegues, we are glad to announce the new release of VEGA1.4.2 ( http://users.unimi.it/ddl ) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of VEGA1.4.2: - PowerNet plugin: TCP/IP protocol, PDB direct connection, script managment interface. - REBOL scripting language. Some scripts are included in the package. - AMD Athlon/Duron and Pentium 4 optimizations. - Edit atom dialog box. - GAMESS output loader. - Updated Gasteiger-Marsili charge attribution. - Bug fixes and new extended commands. REBOL is a messaging language that provides a broad range of practical solutions to the daily challenges of Internet computing. REBOL offers a new approach to the exchange and interpretation of network-based information over a wide variety of computing platforms. REBOL scripts are as easy to write as HTML or shell scripts: a script can be a single line or an entire application. The PowerNet plugin includes a useful interface to manage the REBOL scripts. Trough these scripts it's possible to control the VEGA function in order to automate the most common and repetitive operations. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/ddl From chemistry-request@server.ccl.net Wed Sep 4 08:33:08 2002 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g84CX8311653 for ; Wed, 4 Sep 2002 08:33:08 -0400 To: chemistry@ccl.net Subject: Accelrys Macromolecular Modeling Workshops in San Diego MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.10 March 22, 2002 Message-ID: From: tluu@accelrys.com Date: Wed, 4 Sep 2002 13:33:02 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 09/04/2002 12:33:08 PM, Serialize complete at 09/04/2002 12:33:08 PM Content-Type: multipart/alternative; boundary="=_alternative 0044F15680256C2A_=" This is a multipart message in MIME format. --=_alternative 0044F15680256C2A_= Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding a pair of 2-day workshops at our office in San Diego, October 29 through November 1, 2002. On October 29-30, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On October 31-November 1, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are $1200 commercial, $900 government, and $660 academic. Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Elizabeth Crookenden +44 (0) 1223 228691 --=_alternative 0044F15680256C2A_= Content-Type: text/html; charset="us-ascii"
Accelrys Inc. will be holding a pair of 2-day workshops at our office in San Diego, October 29 through November 1, 2002.

On October 29-30, the workshop "Introduction to Life Science Modeling with InsightII" will be offered.  This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment.  Prior modeling experience is not assumed making this course a great place to start molecular modeling.

On October 31-November 1, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step.  Both manual and automatic methodologies will be discussed.  Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII.

Fees for each 2-day course are $1200 commercial, $900 government, and $660 academic.

Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php.  Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html).  Please do not hesitate to contact us should you have any questions.

Thank you very much.

Jeffrey L. Nauss
858-799-5555

Elizabeth Crookenden
+44 (0) 1223 228691
--=_alternative 0044F15680256C2A_=-- From chemistry-request@server.ccl.net Wed Sep 4 10:45:32 2002 Received: from alcides.host4u.net ([216.71.64.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g84EjW315842 for ; Wed, 4 Sep 2002 10:45:32 -0400 Received: from saturn.simbiosys.ca (CPE014140015690.cpe.net.cable.rogers.com [24.157.155.189] (may be forged)) by alcides.host4u.net (8.11.6/8.11.6) with ESMTP id g84EjLV27540; Wed, 4 Sep 2002 09:45:22 -0500 Received: from simbiosys.ca (mars.simbiosys.ca [192.168.213.5]) by saturn.simbiosys.ca (Postfix) with ESMTP id 53D8FE6D; Wed, 4 Sep 2002 10:45:11 -0400 (EDT) Sender: aniko@simbiosys.ca Message-ID: <3D761C77.1E98BD25@simbiosys.ca> Date: Wed, 04 Sep 2002 10:45:11 -0400 From: Aniko Simon Organization: SimBioSys Inc. X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.8-26mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: "parthi.s" Cc: chemistry@ccl.net Subject: Re: CCL:Image to molecular structure References: <200209030615.g836FUQ24949@jubilantbiosys.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Parthiban, Yes, there is a program exactly for that purpose. See program called: CLiDE (Chemical Literature Data Extraction) more info @: http://www.simbiosys.ca/clide/ Regards, Aniko -- Aniko Simon Ph.D. t: (416) 741 4263 e: aniko@simbiosys.ca w: http://www.simbiosys.ca/ "parthi.s" wrote: > Dear CClers: > Is there any program that can convert an image of a molecular structure (gif, > jpeg) to molecular structure in some formats like mol2, smiles, car, xyz > and so on. I am sure there would have been some attempt to scan the molecular > structures from journals/patents and convert them in some formats. > Any information in this line would be appreciated. > I will summarise the responses. > Thanks and Regards > S. Parthiban > Jubilant Biosys Ltd. (http://www.jubilantbiosys.com) > #18, SJM Towers, 4th Floor > Sheshadri Road, Gandhinagar > Bangalore 560 009 INDIA > Tel: 220 7301 to 220 7309 > Fax: 220 7310 > > -= 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 Wed Sep 4 12:22:22 2002 Received: from abello.unab.cl ([200.27.72.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g84GMK318579 for ; Wed, 4 Sep 2002 12:22:21 -0400 Received: from quimanche (router_republica.unab.cl [200.27.72.5]) by abello.unab.cl (8.11.6/8.11.6) with SMTP id g84GLfQ25786 for ; Wed, 4 Sep 2002 12:21:41 -0400 From: "Ramiro Arratia" To: Subject: 3rd Workshop of Computational Chemistry & Molecular Spectroscopy Date: Wed, 4 Sep 2002 12:21:50 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear Colleagues, This is to remind you tat the deadline for receiving constributions for the 3rd Workshop of Computational Chemistry and Molecular Spectroscopy is September 15, 2002. We invite you to submit your contributions to p.perez@unab.cl or echamorro@unab.cl Please visit our web page at www.unab.cl/workshop/ Sincerely yours, Ramiro Arratia-Perez, Ph.D. Director Area de Ciencias Quimicas Universidad Andres Bello Republica 217 Santiago, CHILE phone: (562)-661-8232 Fax: (562)-661-5679 rarratia@unab.cl From chemistry-request@server.ccl.net Wed Sep 4 15:44:17 2002 Received: from maverick.arl.army.mil ([128.63.58.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g84JiG323342 for ; Wed, 4 Sep 2002 15:44:17 -0400 Subject: Second Internet Bridge Computational Chemistry Workshop To: CHEMISTRY@ccl.net X-Mailer: Lotus Notes Release 5.0.4a July 24, 2000 Message-ID: From: "Mark Zottola - Contractor" Date: Wed, 4 Sep 2002 15:43:36 -0400 X-MIMETrack: Serialize by Router on Maverick/arl(Release 5.0.9a |January 7, 2002) at 09/04/2002 03:43:44 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii SURA Computational Chemistry Workshop "Software Solutions to Large Scale Problems in Computational Chemistry" University of Kentucky, Lexington, Kentucky October 7 & 8, 2002 The National Science Foundation (NSF), Southeastern Universities Research Association (SURA), the University of Kentucky and the Army Research Laboratory (ARL) are pleased to announce the Second Internet Bridge Computational Chemistry Workshop. This workshop seeks to provide a showcase for the frontiers of computational chemistry and will take advantage of the advances in VRVS, allowing for state-of-the-art knowledge to be presented with state-of-the-art technology. Exploring the future of computational chemistry, this workshop will discuss alternatives for mapping computational chemistry software on to the new generation of Terascale machines. Since the National Science Foundation is building the ETF (Extended Terascale Facility) aka the Teragrid, the key question for computational chemistry is "How can computational chemistry take advantage of the Teragrid to solve very large scale problems?" To answer that question, the organizers have invited leaders in both quantum mechanics and bio-informatics to speak, including Dr. Bill Goddard (Cal Tech), Dr. Lawrence Delucas (UAB) and Dr. HF Schaeffer III (UGa). In addition, developers of some of the most widely used quantum codes will speak on their products such as Dr. Theresa Windus of Pacific Northwest Laboratories (NWChem) and Dr. Rodney Bartlett of the University of Florida (ACES II). This workshop will be held October 7 and 8 at the University of Kentucky. and will be using VRVS technology to link Mbone and H.323 technologies into a single distributed environment Registration and information for this event is at http://www.sura.org/events/2001/compchem/chemistry02.html . Attendance via internet can also be accomplished by registering your site.in the registration form. Posters are welcome. Please submit a 200-300 word abstract to Sue@SURA.org. before October 1st. Presentations are scheduled for Monday, October 7th, 6:30pm during the reception in the Hardymon Building on campus.