From chemistry-request@ccl.net Mon Jun 2 22:03:57 2003 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5323ugC015699 for ; Mon, 2 Jun 2003 22:03:57 -0400 Received: from [128.97.147.213] (ch-13.psnet.ucla.edu [128.97.147.213]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id h5323o7s032243; Mon, 2 Jun 2003 19:03:52 -0700 Mime-Version: 1.0 X-Sender: scerri^at^chlorine.chem.ucla.edu (Unverified) Message-Id: In-Reply-To: <200306021832.h52IWQCR022260^at^smtp1.server.rpi.edu> References: <200306021832.h52IWQCR022260^at^smtp1.server.rpi.edu> Date: Mon, 2 Jun 2003 19:03:48 -0700 To: "Dr. N. SUKUMAR" From: Eric Scerri Subject: Re: CCL:orbitals Cc: ccl Content-Type: multipart/alternative; boundary="============_-1157516664==_ma============" --============_-1157516664==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" >On Fri, 6 Jun 2003 23:37:27 -0700 Eric Scerri wrote: > >> >> But far more obviously the anti-realistic view was adopted because so >> many QM concepts seem to defy a realistic interpretation. Is the >> electron a wave or a particle? The electron has no definite >> trajectory. Electron spin is not really spin, Collapse of the >> wavefunction issue etc etc. >> > >This is again a meaningless classification in this day and age. I was trying to get at the origins of anti-realism in quantum mechanics. This is a historical question for which the views of the founders are in fact relevant. >Which >Almighty Being declared that everything has to be a particle or a wave? An >electron is an electron, just as an elephant is an elephant. Is an elephant >a pillar or a rope? It has a massive leg like a pillar, but a flexible tail >like a rope. This does not imply any pillar-rope duality. > >The closest I can think of to such an Almighty Being was Neils Bohr, the >Creator of the Copenhagen Interpretation. But waves and particles were just >everyday objects to give early 20th century physicists an intuitive feel >for difficult quantum mechanical concepts, to "explain" these concepts to >people of that generation (but I use this term rather warily, because many >consider an "explanation" as something absolute, rather than tentative: one >way of seeing things). Now two or more generations of students have grown >up "seeing" electrons on their TV screens and computer monitors, whereas >many are the inner city youth who have never seen a water wave in a lake or >sea. Bohr held the view that quantum objects always had to be formulated in >terms of classical everyday language. But as we all know, the everyday >language of today is not Bohr's classical language. Isn't it time to rework >these tired 20th century laymen's analogies? It is so easy to criticize the founders of any theory with the benefit of hindsight. >Now in terms of mathematics, of course, we have Newtonian mechanics under >one set of limiting conditions and Newtonian (physical) optics under >another. But this does not mean that an electron is a particle or a wave or >a particle when you look and a wave when you don't. > >> > > >> You did not explain why you felt that your example was "better" than >> phlogiston. >> >> > >OK, not "better"; just more convenient for my argument :-) > >> >> ... As Popper himself stated, "All theories >> are born refuted", meaning that sooner or later they will all be >> refuted. Scientific theories are only provisionally useful. Every >> single one of them will eventually be refuted. This is a >> meta-induction based on the fate of all past and now defunct theories >> from the history of science... > >But this itself is only a theory and hence is "born refuted". That makes it >a self-refuting argument. Actually no since it is a philosophical idea not a scientific theory. Popper readily admitted that his own philosophical views were not refutable and are therefore not scientific. That does not diminish the force of his philosophical analysis which incidentally I thought you rather approved of. > >> >> Of course one may argue that induction from past instances is not a >> reliable path to knowledge and that it just so happens that our >> cherished current theories have finally reached the point where they >> are refutable but will never actually be refuted. But that would be >> plain stupid of course. >> >> > >I myself donot disagree with your belief, but it is just that: a BELIEF. A belief founded on the fate of every old theory that has now been refuted. A belief as much as any scientific law or theory which has been established by induction. And that applies to all observational laws of course. >Those who believe otherwise and seek the "ultimate" Theory of Everything or >Hoheberg and Kohn's Universal Functional are NOT plain stupid. People who seek theories of everything almost invariably then say that they don't really mean a theory of EVERYTHING. In any case a theory of everything does not imply a theory that will survive for ever. It is quite possible to explain our current "everything" but that the future will expand out notion of everything such that the old theory of everything will need to be abandoned. I assume that similar things could be said about Hohenberg and Kohn's Universal Function. >150 years >ago, one could have said that all attempts by humans to achieve powered >flight had failed and thus, by meta-induction, all future attempts would be >doomed to failure. Likewise for all attempts throughout human history to >transmute elements. Yes good examples but not of the same kind. My own meta-induction does not involve specifics. It is a statement about all theories > >There are so many variables. If the federal governments stop funding high >energy physics altogether, as they are quite likely to sooner or later, or >if humanity does not survive into the next century, then the Standard Model >of physics may never be refuted (with apologies to Popper). Does any of >this make the Standard Model any more "true"? A meaningless question, in my >opinion. yes you have answered your own question very well. eric scerri > > > > >Dr. N. Sukumar -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri^at^chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --============_-1157516664==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL:orbitals
On Fri, 6 Jun 2003 23:37:27 -0700 Eric Scerri wrote:

>
> But far more obviously the anti-realistic view was adopted because so
> many QM concepts seem to defy a realistic interpretation.  Is the
> electron a wave or a particle?  The electron has no definite
> trajectory.  Electron spin is not really spin, Collapse of the
> wavefunction issue etc etc.
>

This is again a meaningless classification in this day and age.


I was trying to get at the origins of anti-realism in quantum mechanics.  This is a historical question for which the views of the founders are in fact relevant. 

Which
Almighty Being declared that everything has to be a particle or a wave? An
electron is an electron, just as an elephant is an elephant. Is an elephant
a pillar or a rope? It has a massive leg like a pillar, but a flexible tail
like a rope. This does not imply any pillar-rope duality.

The closest I can think of to such an Almighty Being was Neils Bohr, the
Creator of the Copenhagen Interpretation. But waves and particles were just
everyday objects to give early 20th century physicists an intuitive feel
for difficult quantum mechanical concepts, to "explain" these concepts to
people of that generation (but I use this term rather warily, because many
consider an "explanation" as something absolute, rather than tentative: one
way of seeing things). Now two or more generations of students have grown
up "seeing" electrons on their TV screens and computer monitors, whereas
many are the inner city youth who have never seen a water wave in a lake or
sea. Bohr held the view that quantum objects always had to be formulated in
terms of classical everyday language. But as we all know, the everyday
language of today is not Bohr's classical language. Isn't it time to rework
these tired 20th century laymen's analogies?


It is so easy to criticize the founders of any theory with the benefit of hindsight. 



Now in terms of mathematics, of course, we have Newtonian mechanics under
one set of limiting conditions and Newtonian (physical) optics under
another. But this does not mean that an electron is a particle or a wave or
a particle when you look and a wave when you don't.

>
>
> You did not explain why you felt that your example was "better" than
> phlogiston.
>
>

OK, not "better"; just more convenient for my argument :-)

>
> ...  As Popper himself stated, "All theories
> are born refuted", meaning that sooner or later they will all be
> refuted.  Scientific theories are only provisionally useful. Every
> single one of them will eventually be refuted.  This is a
> meta-induction based on the fate of all past and now defunct theories
> from the history of science...

But this itself is only a theory and hence is "born refuted". That makes it
a self-refuting argument.


Actually no since it is a philosophical idea not a scientific theory. 
Popper readily admitted that his own philosophical views were not refutable and are therefore not scientific.  That does not diminish the force of his philosophical analysis which incidentally I thought you rather approved of. 


>
> Of course one may argue that induction from past instances is not a
> reliable path to knowledge and that it just so happens that our
> cherished current theories have finally reached the point where they
> are refutable but will never actually be refuted.  But that would be
> plain stupid of course.
>
>

I myself donot disagree with your belief, but it is just that: a BELIEF.


A belief founded on the fate of every old theory that has now been refuted. 

A belief as much as any scientific law or theory which has been established by induction.  And that applies to all observational laws of course. 


Those who believe otherwise and seek the "ultimate" Theory of Everything or
Hoheberg and Kohn's Universal Functional are NOT plain stupid.


People who seek theories of everything almost invariably then say that they don't really mean a theory of EVERYTHING.  In any case a theory of everything does not imply a theory that will survive for ever.  It is quite possible to explain our current "everything" but that the future will expand out notion of everything such that the old theory of everything will need to be abandoned. 

I assume that similar things could be said about Hohenberg and Kohn's Universal Function. 


150 years
ago, one could have said that all attempts by humans to achieve powered
flight had failed and thus, by meta-induction, all future attempts would be
doomed to failure. Likewise for all attempts throughout human history to
transmute elements.


Yes good examples but not of the same kind.  My own meta-induction does not involve specifics.  It is a statement about all theories


There are so many variables. If the federal governments stop funding high
energy physics altogether, as they are quite likely to sooner or later, or
if humanity does not survive into the next century, then the Standard Model
of physics may never be refuted (with apologies to Popper). Does any of
this make the Standard Model any more "true"? A meaningless question, in my
opinion.

yes you have answered your own question very well.

eric scerri





Dr. N. Sukumar
--


Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri^at^chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.kluweronline.com/issn/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1157516664==_ma============-- From chemistry-request@ccl.net Mon Jun 2 19:17:24 2003 Received: from sccrmhc12.attbi.com (sccrmhc12.attbi.com [204.127.202.56]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52NHOgC013229 for ; Mon, 2 Jun 2003 19:17:24 -0400 Received: from C1353359A (12-207-205-144.client.attbi.com[12.207.205.144](untrusted sender)) by attbi.com (sccrmhc12) with SMTP id <20030602231722012003ucvde>; Mon, 2 Jun 2003 23:17:22 +0000 Reply-To: From: "Mark Thompson" To: "Van Dam, HJJ \(Huub\)" , Cc: Subject: CCL: Accuracy of RPA linear response calculations Date: Mon, 2 Jun 2003 16:13:03 -0700 Message-ID: <000201c3295c$84513370$0300a8c0^at^attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" 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) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal In-Reply-To: <3EDB6B4C.1050307^at^dl.ac.uk> Dear Huub, > > I am planning to do some large scale calculations of excitation spectra > in the Random Phase Approximation (RPA). However, before I burn fast > amounts of CPU cycles I would like to have a good idea of how sensible I > can expect the results to be (in comparison to experimental results). > Could you suggest some recent review papers on applications of this > theory, please? I will summarize the responses of course. If you choose Look at: J. Phys. Chem. A (2002) 106(44) p. 10596-10605. by Geoff Hutchison et. at. Regarding burning CPU time, the ArgusLab 3.1 implementation of ZINDO/RPA is extremely fast. You can obtain it from http:://www.planaria-software.com Please feel free to send me examples of the types of molecules you intend to study. I'd like to see how they benchmark against some of the systems we've tested. Cheers, Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 ArgusLab is available at: http://www.arguslab.com ================================= > > I am planning to do some large scale calculations of excitation spectra > in the Random Phase Approximation (RPA). However, before I burn fast > amounts of CPU cycles I would like to have a good idea of how sensible I > can expect the results to be (in comparison to experimental results). > > Could you suggest some recent review papers on applications of this > theory, please? I will summarize the responses of course. If you choose > to respond but do not want your response to appear in the summary please > let me know. > > Many thanks, > > Huub van Dam > > -- > > ======================================================================== > > Huub van Dam E-mail: h.j.j.vandam^at^dl.ac.uk > CCLRC Daresbury Laboratory phone: +44-1925-603362 > Daresbury, Warrington fax: +44-1925-603634 > Cheshire, UK mobile: +44-7739-330511 > WA4 4AD > > ======================================================================== > > > > > -= This is automatically added to each message by 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, jkl^at^ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Jun 3 12:29:02 2003 Received: from monteverdi.theochem.ruhr-uni-bochum.de (monteverdi.theochem.ruhr-uni-bochum.de [134.147.125.253]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h53GT1gC003345 for ; Tue, 3 Jun 2003 12:29:02 -0400 Received: from bruckner.theochem.ruhr-uni-bochum.de (IDENT:cboehme..at..bruckner.theochem.ruhr-uni-bochum.de [134.147.125.173]) by monteverdi.theochem.ruhr-uni-bochum.de (8.11.6/8.11.0) with SMTP id h53GT0J32149 for ; Tue, 3 Jun 2003 18:29:00 +0200 Date: Tue, 3 Jun 2003 18:29:00 +0200 From: Christian Boehme To: "chemistry..at..ccl.net" Subject: CCL: Summary: Viewmol problem / IR data visualization Message-Id: <20030603182900.7c934210.Christian.Boehme..at..uni-bochum.de> X-Mailer: Sylpheed version 0.8.11claws (GTK+ 1.2.9; i686-pc-linux-gnu) Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h53GT2gC003348 Dear all, this is the summary for the following original questions: [I want to use Viewmol for IR data visualization, because it imitates the look of experimental spectra. I compiled version 2.3 from the sourceforge website without problems (the binaries did not work for me). However, each file loading attempt, including the contained examples, results in a "wrong file type error", even if I specify the type on the command line. Does anyone have an idea what's wrong? Alternatively, does anyone know another program which shows Gaussian98 calculated IR spectra in a way resembling an experimental spectrum, preferably under Linux? I think this question has been asked before, but I did not find it in the archives. WebMO is not a good solution for me, because of the webserver requirements.] 1. Regarding viewmol it was suggested to try setting the system language of my linux box to English, which did not help. 2. As alternatives for IR specra visualization I got the following recommendations: - SWizard (Windows NT/2000/XP): http://www.obbligato.com/software/swizard/ (Looks nice, but I did not test it because it is for Windows only) - MOLDRAW (Windows): http://www.chimifm.unito.it/fisica/moldraw/avail.html (Also not tested) - From CCL: http://www.ccl.net/cca/software/SOURCES/C/IR-spectrum/index.shtml (Together with a little bit of perl scripting and Grace (http://plasma-gate.weizmann.ac.il/Grace/) this is what I ended up using) Here are the (slightly shortened) original answers: > From Matthias Mann : [Hi Christian, in my case the same problem was due to an different language environment. I compiled Viewmol 2.3 under SuSE Linux 8.0 (english environment) and it doesn't run under the complete same installation with german environment. Changing the system language solved the problem. Generally, the program seems to be very sensitive to installation changes, e.g. the path to the executables and convert scripts. So I had the same error also in case of changing the installation path, although I adjusted the VIEWMOLPATH variable. You should try to compile, install and use the program on the same system with default path structure. Matthias -- Dr. Matthias Mann Fachrichtung Chemie, TU Dresden, D-01062 Dresden Tel./Fax: +49 (351) 463-34286 Email: Matthias.Mann..at..chemie.tu-dresden.de] > From "S. I. Gorelsky" : [Hello, This program can help: http://www.obbligato.com/software/swizard/ it will process G98 files with IR data. With regards, S. Gorelsky] > From Bartolomeo Civalleri : [Dear Christian, I would like to suggest you to try the MOLDRAW program, available free of charge, from: http://www.chimifm.unito.it/fisica/moldraw/avail.html You can import a G98 frequency calculation output and then you can both animate the vibrational normal modes and simulate either a IR or a Raman spectra. All the best Mimmo Dr Bartolomeo Civalleri Dipartimento di Chimica IFM, Universita' di Torino Via P. Giuria 7 I-10125 Torino (Italy) Phone: +39-011-6707564 Fax: +39-011-6707855 E-mail: bartolomeo.civalleri..at..unito.it] From: "Jeremy R. Greenwood" : [Hi Christian, I use a trivial amount of scripting and spectrum.c http://www.ccl.net/cca/software/SOURCES/C/IR-spectrum/index.shtml to create discrete data, then paste the output into a spreadsheet and graph it. Works for me. You should be able to do it with gnu/Linux. Hope this helps, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy..at..greenwood.net Department of Medicinal Chemistry bh +45 35306117 The Danish University of Pharmaceutical Sciences fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- ] -- Dr. Christian Boehme Lehrstuhl f|r theoretische Chemie Private: Ruhr-Universitdt Bochum Dorstener Str. 40 44780 Bochum 44787 Bochum Germany Germany email:Christian.Boehme..at..theochem.uni-bochum.de email:ChristianBoehme..at..web.de phone:+49-(0)234-32 22121 phone:+49-(0)234-3243655 fax: +49-(0)234-32 14045 fax: +49-(0)234-3246741 From chemistry-request@ccl.net Tue Jun 3 06:05:45 2003 Received: from huygens.rijnh.nl (huygens.rijnh.nl [192.42.124.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h53A5igC025836 for ; Tue, 3 Jun 2003 06:05:45 -0400 Received: from [192.42.124.115] (macgvh.rijnh.nl [192.42.124.115]) by huygens.rijnh.nl (SGI-8.12.5/8.12.5) with ESMTP id h53A8Von2058534; Tue, 3 Jun 2003 12:08:31 +0200 (MET_DST) Mime-Version: 1.0 X-Sender: gertvh..at..huygens.rijnh.nl Message-Id: In-Reply-To: <3ED5A324.B8CC04AE..at..wyoming.com> References: <000001c325a1$4a9384d0$0300a8c0..at..attbi.com> <3ED5A324.B8CC04AE..at..wyoming.com> Date: Tue, 3 Jun 2003 12:07:25 +0200 To: Philip Stortz , chemistry..at..ccl.net From: Gert von Helden Subject: Re: CCL:Crystal building tools Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear Philip, I use CrystalMaker (http://www.crystalmaker.co.uk). It is a great program to generate, visualize and manipulate Crystals. I use it and am very happy with it. One potential problem for you might be that it only runs on Macintosh. Hope that helps, Gert At 00:05 -0600 29/5/03, Philip Stortz wrote: >To help with modeling electronic spectra of crystals, is there a >good package out there to build the initial crystal with at least a >couple dozen unit cells if i know the crystal structure? I've tried >this with Cache a few years ago, and the drawing tool was not very >useful and very painful for building 3d crystals, bonds often wound >up in odd places where i didn't mean to put them and it was very >hard to view the bonds to see these problems. Thanks again. > >-- >Philip Stortz -- To be nobody but yourself when the whole world is >trying its best night and day to make you everybody else is to fight >the hardest battle any human being will ever fight. -- E.E. Cummings > > >-= This is automatically added to each message by 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, jkl..at..ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- ******************************************************* Gert von Helden FOM Institute for Plasmaphysics Rijnhuizen Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands http://www.rijnh.nl/ e-mail: gertvh..at..rijnh.nl phone: (+31) 30 6096999, fax: (+31) 30 6031204 From chemistry-request@ccl.net Tue Jun 3 08:00:22 2003 Received: from ursa.calvin.edu (ursa.calvin.edu [153.106.4.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h53C0MgC028860 for ; Tue, 3 Jun 2003 08:00:22 -0400 Received: from gwise.calvin.edu (gwise.calvin.edu [153.106.4.30]) by ursa.calvin.edu (8.11.6p2/8.11.6) with ESMTP id h53C0LG22999 for ; Tue, 3 Jun 2003 08:00:21 -0400 (EDT) Received: from Calvin-MTA by gwise.calvin.edu with Novell_GroupWise; Tue, 03 Jun 2003 08:00:22 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.0 Date: Tue, 03 Jun 2003 08:00:12 -0400 From: "Roger L. DeKock" To: Subject: CCL:orbitals Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-7 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h53C0MgC028861 Pertinent to this discussion is the following book: Making Truth: Metaphor in Science Theodore L. Brown University of Illinois Press 2003 /------------- Roger L. DeKock Calvin College From chemistry-request@ccl.net Tue Jun 3 11:30:25 2003 Received: from web15207.mail.bjs.yahoo.com (web15207.mail.bjs.yahoo.com [202.3.77.137]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h53FUKgC001694 for ; Tue, 3 Jun 2003 11:30:23 -0400 Message-ID: <20030603153009.21413.qmail=at=web15207.mail.bjs.yahoo.com> Received: from [218.26.230.10] by web15207.mail.bjs.yahoo.com via HTTP; Tue, 03 Jun 2003 23:30:09 CST Date: Tue, 3 Jun 2003 23:30:09 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: Two questions about molecular size To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I have two questions during my study on beta-cyclodextrin. Some literatures give the high, diameter and volume of the cavity. I hope to know how to get those parameters? By calculation, or other methods? Dose anyone here like to give me some hints? Another problem is how to calculate the volume of a substitute of an organic molecule? Thank you very much in advance! Regards, Jinsong _________________________________________________________ Do You Yahoo!? AwA,MxBgJ@=g5D!0Dc!1JGK-#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/cn_user_profile_study_may2003 From chemistry-request@ccl.net Tue Jun 3 14:34:26 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h53IYOgC007712 for >ccl.net>; Tue, 3 Jun 2003 14:34:25 -0400 Received: from [131.202.166.40] (tibook.chem.unb.ca [131.202.166.40]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h53IYJXd031604 for >ccl.net>; Tue, 3 Jun 2003 15:34:19 -0300 User-Agent: Microsoft-Entourage/10.1.1.2418 Date: Tue, 03 Jun 2003 15:34:16 -0300 Subject: CCL: Homology model of SARS protein From: Ghislain Deslongchamps >unb.ca> To: >ccl.net> Message-ID: >unb.ca> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=0, required 7, SPAM_PHRASE_00_01, USER_AGENT, USER_AGENT_ENTOURAGE) Hi folks, We have developed a homology model of SARS protein "SARS-CoV Mpro" using MOE 2003.02. This work was done independently of the model recently reported by Hilgenfeld. An HTML article, including pdb coordinates, is available at http://biocomp.chem.unb.ca. Hopefully this will be of use to the SARS-minded comp chem community. All the best, -Ghislain ----------------------------------------------------------- Dr. Ghislain Deslongchamps, Professor Department of Chemistry, Faculty of Science University of New Brunswick Fredericton, N.B. CANADA E3B 6E2 phone: (506) 453-4795 cell: 470-9976 FAX: 453-4981 e-mail: ghislain<>unb.ca WWW: http://biocomp.chem.unb.ca -----------------------------------------------------------