From chemistry-request@server.ccl.net Sun Jul 22 02:31:05 2001 Received: from smtp1.post.cz ([195.250.146.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6M6V5518827 for ; Sun, 22 Jul 2001 02:31:05 -0400 Received: (from root@localhost) by smtp1.post.cz (8.11.2/8.11.2/Debian 8.11.2-1) id f6M6V4508708; Sun, 22 Jul 2001 08:31:04 +0200 From: sasha1@post.cz X-Priority: 1 MIME-Version: 1.0 Message-Id: <3B5A7328.000001.08706@smtp1> Date: Sun, 22 Jul 2001 08:30:27 +0200 (CEST) Content-Type: Text/Plain Content-Transfer-Encoding: 7bit To: chemistry@ccl.net Subject: A useful tutorial on designing high-energy species Recently somebody asked the CCL list for some instructive computational illustrations for energy-rich compounds. Here is an interesting tutorial: http://www.findarticles.com/m2843/4_24/63693001/p1/article.jhtml revealing relatively common conceptual mistakes. From chemistry-request@server.ccl.net Sun Jul 22 15:48:23 2001 Received: from mum.mans.eun.eg ([193.227.50.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6MJmL522522 for ; Sun, 22 Jul 2001 15:48:22 -0400 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id ; Sun, 22 Jul 2001 22:51:55 +0300 Message-ID: <4EF2E03A9B67D2119E2E0000F8053499427565@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'chemistry@ccl.net'" Subject: qsar-question Date: Sun, 22 Jul 2001 22:51:53 +0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C112E7.C2A94555" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C112E7.C2A94555 Content-Type: text/plain Dear Netteres; QSARER's I have calculated lots of descriptors for a training set. When trying to find out the correlation between each descriptor and the experimental activity (toxicity), one can not find any reasnable correlation for any descriptor ( always, R^2<0.01). Could you please make any suggestions? Regards Tarek ------_=_NextPart_001_01C112E7.C2A94555 Content-Type: text/html Content-Transfer-Encoding: quoted-printable qsar-question

Dear Netteres; QSARER's
I have calculated lots of descriptors = for a training set. When trying to find out the correlation between = each descriptor and the experimental activity (toxicity), one can not = find any reasnable correlation for any descriptor ( always, = R^2<0.01).

Could you please make any = suggestions?
Regards
Tarek

------_=_NextPart_001_01C112E7.C2A94555-- From chemistry-request@server.ccl.net Sat Jul 21 14:49:16 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6LInG513284 for ; Sat, 21 Jul 2001 14:49:16 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id NAA21945 for ; Sat, 21 Jul 2001 13:48:31 -0500 (CDT) Date: Sat, 21 Jul 2001 13:48:31 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks for the previous answers. They were quite helpful. I have a question about the naming. for example in PHEnylalanine( given below), there are two 'CD' and two 'CE's. Does the order matter, i mean is the left Carbon to the C(CG) CD1 or the right Carbon? thanks vani C <-------CA | CH2 <------CB | C <------CG / \\ HC CH <---- CD1, CD2 || | HC CH <----- CE1, CE2 \ // CH <------CZ From chemistry-request@server.ccl.net Sun Jul 22 20:18:15 2001 Received: from mta1.263.net ([202.96.44.43]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6N0I0524522 for ; Sun, 22 Jul 2001 20:18:00 -0400 Received: by mta1.263.net (Postfix, from userid 60001) id BABB11C70E248; Mon, 23 Jul 2001 07:59:15 +0800 (CST) Message-Id: <3B5B68D3.06124@mta1> Date: Mon, 23 Jul 2001 07:59:15 +0800 (CST) From: "刘鑫杰" To: chemistry@ccl.net Subject: Does anyone knows the RAS-SCF? X-Priority: 3 X-Originating-IP: [166.111.26.197] X-Mailer: COREMAIL Hello,everyone! Does anyone knows the RAS-SCF(Restricted Active Space-Self Consistent Field) theory? What is the RAS1,RAS2,RAS3 means?How to design and setup the three space? __________________________________________ IP卡、上网卡全线跳水价 http://shopping.263.net/category08.htm 古埃及订情饰物订做 http://shopping.263.net/category11.htm From chemistry-request@server.ccl.net Sun Jul 22 15:16:51 2001 Received: from mr3.cc.ic.ac.uk ([155.198.5.113]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6MJGo522312 for ; Sun, 22 Jul 2001 15:16:50 -0400 Received: from icex9.cc.ic.ac.uk ([155.198.3.9]) by mr3.cc.ic.ac.uk with esmtp (Exim 3.31 #1) id 15OOig-0004Wd-00; Sun, 22 Jul 2001 20:16:50 +0100 Received: from [155.198.234.86] (rzepa.ch.ic.ac.uk [155.198.234.86]) by icex9.cc.ic.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id P10Z5SGP; Sun, 22 Jul 2001 20:16:50 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: Date: Sun, 22 Jul 2001 20:16:01 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: XML-CML Software/Demo on http://www.xml-cml.org/ Content-Type: text/plain; charset="us-ascii" We would like to announce the availability of a new release of JUMBO3, (which can be expanded to Java Universal Molecular Browser), which is an XML-based software toolkit illustrating working examples of CML. CML (Chemical Markup language) is the most mature and best developed and documented Chemical application of XML, and we have now made available an extensive range of resources and software tools to illustrate its form and its application, together with a list of some "frequently asked questions" about CML and XML The materials include 1. A (2 Mbyte) free download for the JUMBO3-J browser written by Peter Murray-Rust, which is a standalone molecular browser written in Java (1.2 compatible) and capable of reading not only CML files, but a wide range of legacy molecular formats. This browser includes the excellent JMVS 3D viewer written by Allistair Crossley and incorporated into JUMBO3 as an example of how such software can be easily extended via collaboration. This requires the installation of the Java3D run time library.. The download also includes source code for the core components of CML for the developers amongst you 2. An on-line demo and (400K) download for a lightweight version of JUMBO3 written in JavaScript by Peter and Michael Wright, which is capable of viewing XML-CML files by converting them on the fly to SVG, which is then displayed using Adobe's SVG viewer. This is an excellent illustration of how XML data can be transformed into other XML forms (SVG is also XML), in this case for display purposes 3. An on-line demo for a CML aware version of the Peter Ertl's Java Molecular Editor (JME).. The base JME editor is extended using an interface (JMECML) to input and output CML as well as the usual JME supported formats. It comes as an application (which allows CML files to be read and written to local hard disk) and an applet (which allows CML files to be copied to the clipboard for pasting into other applications). 4. We have compiled an FAQ which attempts to address many of the questions and issues often raised in connection with XML and CML. This is an on going project, and we expect will be extensively added to over the coming months, we hope via the questions and FAQs that you send us! If anyone has other examples of the use of CML and chemical applications of XML in general please let us know and we can include them on our pages (there are several excellent examples already out there, including the SelfML browser for physico chemical data written by Peter Murray-Rust and also available on-line for demonstrations at the site, and CrocZilla, part of the Mozilla project to extend the Netscape browser into XML). Its all up at http://www.xml-cml.org/ Peter Murray-Rust and Henry Rzepa.