From chemistry-request@ccl.net Fri Dec 17 18:56:33 2004 Received: from out-mail04.yourhostingaccount.com (mailrelay1.yourhostingaccount.com [38.113.1.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBHNuVXa007132 for ; Fri, 17 Dec 2004 18:56:31 -0500 Message-Id: <200412172356.iBHNuVXa007132..at..server.ccl.net> Received: from scan03.yourhostingaccount.com ([10.1.1.233] helo=scan03.yourhostingaccount.com) by mail04.yourhostingaccount.com with esmtp (Exim) id 1CfSCr-00030E-J2 for chemistry..at..ccl.net; Fri, 17 Dec 2004 19:12:21 -0500 Received: from r2d2.yourhostingaccount.com ([10.1.1.178] ident=exim) by scan03.yourhostingaccount.com with spamscanlookuphost (Exim) id 1CfSCr-0006AB-0A for chemistry..at..ccl.net; Fri, 17 Dec 2004 19:12:21 -0500 Received: from r2d2.yourhostingaccount.com ([10.1.1.178] helo=smtp.yourhostingaccount.com) by scan03.yourhostingaccount.com with esmtp (Exim) id 1CfSCq-0006A5-Od for chemistry..at..ccl.net; Fri, 17 Dec 2004 19:12:20 -0500 Received: from ssf.delsci.net ([66.43.118.66] helo=Hummer) by smtp.yourhostingaccount.com with esmtpa (Exim 4.43) id 1CfSCq-0001Ht-4O ; Fri, 17 Dec 2004 19:12:20 -0500 From: "Warren DeLano" To: , , Cc: "'Miguel'" , , Subject: FW: Jmol version 10.00 - RELEASED Date: Fri, 17 Dec 2004 16:12:07 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcTkf44lxOUs5TX+SeqQTUp7an4ljwAAa2mw X-UserInfo: dfab58b57aa3bb910bf055c23b06c5c7:c10f421fef69a2b5fe207cfa50def74f X-User: warren_1 Sender: "Warren DeLano" X-Spam-Status: No, hits=2.8 required=7.5 tests=CLICK_BELOW,IMPRONONCABLE_1, OFFER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net PyMOL Users & Friends, There is a new kid on the block and he packs quite a punch. His name is Jmol v10 and all who have been looking to put molecular graphics content into a browser or Java applet need to take a close look at this cool new tool. It is a well-engineered free and open-source replacement to Chime available under the LGPL license. Unlike PyMOL, Jmol supports Chime scripts out of the box. Plus, Jmol has a fast software-based renderer that even Roger Sayle would be proud of. Probably the best way to try Jmol is to head on over to the PDB's new beta site: and type in the 4-digit PDB code of your favorite structure at the top of the screen. One that's submitted, click on the Jmol tab right below the structure image. Jmol will open up momentarily. http://www.jmol.org is the main site where you can find more info and demos. One might ask why I draw so much attention to a product that could ostensibly compete with PyMOL. Well, here at DeLano Scientific LLC we utterly reject the notion that competitive concerns could ever provide a legitimate excuse to promote an inferior product we offer over something better from another source. That kind of customer dis-service provides no lasting benefit to anyone, especially within the scientific community. However, I am NOT saying that PyMOL is inferior to Jmol -- they just have different strengths. If you need fast live 3D molecules in a Web page or Java app today, DeLano Scientific does not even offer a solution for that yet. Jmol is a great tool you can adopt right now, and it is ideal if you already have Chime-based content ready to go. It's also worth pointing out that Jmol is one of the few compelling choices that fully complies with the same open-source principles that the PyMOL Open-Source Project adheres to: unrestricted usage, modification, and redistribution for all parties and for all purposes. PyMOL and Jmol aren't about competition, they're about addressing important unmet needs in industry and academia through open-source development and mutually-beneficial relationships between developers and users. There are no legal, business, or philosophical barriers to prevent creation of substantial interoperability between these two packages, either before or after the marketplace demands it. Delano Scientific LLC salutes Miguel, Egon, Chris, and the other Jmol developers for a job well done. There is a lot to the success of the Jmol project that the PyMOL effort could learn from -- whole number releases being just one small example ; ). I hope that Jmol and PyMOL can be used together with other tools like GROMACS, APBS, and MMTK to build new and more flexible ways of meeting your important scientific software needs. Furthermore, I think I can safely speak for all of us in asking that you all follow through when you are presented with the opportunity to help support open-source development, whether through subscription purchases, donations, capital contributions, grant approvals, or by simply citing the open-source tools you use in publications and presentations. Happy Holidays everyone! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren..at..delsci.com Subject: Jmol version 10.00 - RELEASED Jmol version 10.00 was officially released on Friday 17 December 2004. I encourage you to visit http://www.jmol.org, download it, and take a look at it. Jmol is now a viable, fully functional, high performance, open source replacement for the Chime plugin. Those of you who have made investments in RasMol/Chime scripts over the years should now take a serious look at Jmol ... especially those of who who have build web tutorials and applications around the Chime plugin. On a personal note ... I have been working on this release full-time for two years ... so this is clearly a very important milestone for me. And I believe that it is important for the molecular visualization community. Those of you who have made investments in RasMol/Chime scripts, and especially in Chime web courseware, now have a migration path to an open source alternative, an applet written in Java, that does not require installation on the client, that runs on most major web browsers. I undertook this project under the encouragement of Dr. Jose Luis Lopez Perez at the University of Salamanca. Those who will use Jmol and benefit > from it owe Jose Luis a debt of gratitude. !Gracias amigo! Miguel From chemistry-request@ccl.net Fri Dec 17 13:05:38 2004 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBHI5aLI014230 for ; Fri, 17 Dec 2004 13:05:37 -0500 Importance: Normal X-Priority: 3 (Normal) Expiry-Date: Tue, 1 Mar 2005 -1:-1:-1 +0000 Reply-To: workshops(at)accelrys.com To: CHEMISTRY(at)ccl.net Subject: CCL: Accelrys Customer Training for February MIME-Version: 1.0 Sensitivity: X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Jeff Nauss Date: Fri, 17 Dec 2004 10:21:25 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 12/17/2004 10:21:26 AM, Serialize complete at 12/17/2004 10:21:26 AM Content-Type: multipart/alternative; boundary="=_alternative 0064D5C688256F6D_=" X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_20_30,HTML_MESSAGE, MK_BAD_HTML_04 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 multipart message in MIME format. --=_alternative 0064D5C688256F6D_= Content-Type: text/plain; charset="US-ASCII" Accelrys Inc. are holding the following training workshops during February. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. Materials Modeling Introduction to MS Modeling 31 January Burlington, MA Introduction to Polymer Modeling 1-2 February Burlington, MA Introduction to QM Modeling 3-4 February Burlington, MA Introduction to MS Modeling 21 February Cambridge, UK Introduction to QM Modeling 22-23 February Cambridge, UK Introduction to Polymer Modeling 24-25 February Cambridge, UK Intro to Crystal Structure Modeling 28 February to 1 March Cambridge, UK For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html Macromolecular Modeling Introduction to InsightII 1-2 February San Diego, CA Homology Based Protein Design 3-4 February San Diego, CA SBDD with InsightII 7-8 February San Diego, CA CHARMm 9-10 February San Diego, CA Modeling of GPCR Proteins with InsightII 11 February San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Rational Drug Design Introduction to Cerius2 for Life Sciences 15-16 February San Diego, CA Small Molecule and Drug Design with Cerius2 17-18 February San Diego, CA Library Design and Analysis 21-22 February San Diego, CA Pharmacophore Generation with Catalyst 23-24 February San Diego, CA For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training --=_alternative 0064D5C688256F6D_= Content-Type: text/html; charset="US-ASCII"
Accelrys Inc. are holding the following training workshops during February.  These events are designed to help you get more value > from your Accelrys software, helping you to better accomplish your research goals.

Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic.

Materials Modeling

Introduction to MS Modeling           31 January              Burlington, MA
Introduction to Polymer Modeling      1-2 February            Burlington, MA
Introduction to QM Modeling           3-4 February            Burlington, MA
Introduction to MS Modeling           21 February             Cambridge, UK
Introduction to QM Modeling           22-23 February          Cambridge, UK
Introduction to Polymer Modeling      24-25 February          Cambridge, UK
Intro to Crystal Structure Modeling   28 February to 1 March  Cambridge, UK

For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html

Macromolecular Modeling

Introduction to InsightII                 1-2 February   San Diego, CA
Homology Based Protein Design             3-4 February   San Diego, CA
SBDD with InsightII                       7-8 February   San Diego, CA
CHARMm                                    9-10 February  San Diego, CA
Modeling of GPCR Proteins with InsightII  11 February    San Diego, CA

For course details and registration see: http://www.accelrys.com/training/macro/schedule.html

Rational Drug Design

Introduction to Cerius2 for Life Sciences    15-16 February  San Diego, CA
Small Molecule and Drug Design with Cerius2  17-18 February  San Diego, CA
Library Design and Analysis                  21-22 February  San Diego, CA
Pharmacophore Generation with Catalyst       23-24 February  San Diego, CA

For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training
 --=_alternative 0064D5C688256F6D_=-- From chemistry-request@ccl.net Fri Dec 17 11:55:50 2004 Received: from gvedoh01.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBHGtnLI009125; Fri, 17 Dec 2004 11:55:50 -0500 To: "Marcus Martin" Cc: chemistry-.at.-ccl.net, "Computational Chemistry List" Subject: Re: CCL:software for supramolecule building and optimization MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy-.at.-givaudan.com Date: Fri, 17 Dec 2004 18:11:45 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 17/12/2004 18:11:38, Serialize complete at 17/12/2004 18:11:38 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iBHGtoLI009129 Ask a free evaluation copies from each company, test them, then ask prices! Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy-.at.-givaudan.com "Marcus Martin" Sent by: "Computational Chemistry List" 16.12.2004 01:48 To: chemistry-.at.-ccl.net cc: Subject: CCL:software for supramolecule building and optimization On Wednesday 15 December 2004 09:28, andras.borosy-.at.-givaudan.com wrote: > At microscopic level: Materials and Processes Simulations (MAPS) platform > of Scienomics (www.scienomics.com). > Or Material Studio of Accelrys for both (but it does not give you the best > performance/price ratio). How can you tell? While the snapshots on the Scienomics website do look nice I don't see any information about 1) What simulation/quantum codes are actually contained in the MAPS package? 2) How much it costs to purchase MAPS? 3) Exactly which analysis tools are already implemented in this interface? Is this product really available? The only mention of release dates that I found is strictly in the future tense "pleased to announce that it will be releasing the first version of its platform for Materials and Processes Simulations (MAPS) in fall 2004" If anyone out there has the answers to these questions I would be quite interested in hearing them as I have been looking for a good interface to wrap around my Monte Carlo code, but have been disappointed by other folks making similar claims in the past. thanks, Marcus -- Marcus G. Martin Senior Member of Technical Staff Computational Materials and Molecular Biology Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY-.at.-ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+