From ross@cgl.ucsf.EDU  Thu Mar 17 00:42:03 1994
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From: ross@cgl.ucsf.edu (Bill Ross )
To: chemistry@ccl.net
Subject: Example of Web abstract with pictures


This may be of interest as an example of Web scientific
publishing; it's like an abstract with popup color plates.

	http://neuron.arc.nasa.gov/papers/spie_abstract.94/.index.html

Bill Ross

From Leif.Laaksonen@pobox.csc.fi  Thu Mar 17 01:42:02 1994
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To: ross@cgl.ucsf.edu (Bill Ross )
From: Leif.Laaksonen@csc.fi
Subject: Re: CCL:Example of Web abstract with pictures
Cc: chemistry@ccl.net



Bill,

Making Web publications is not that simple. I don't believe that one
can use ordinary text and put links into that. I believe that the whole
text should be written from an other point of view where the links come in
more logically. The text around the links should clearly show WHAT is behind
the link. Other aspects like type of file behind the link, file sizes and
so on should also be seen from the link. We are still living in a world with
slow network connections, after all.

This whole WWW concept is quite difficult to accept by very many because
the way we compete each other is through the publications, more or less.
Giving the publishing away to a neutral publisher we maintain a sort of
neutral territory. Now when the whole business is more up to ourself
it's difficult to find a new neutral territory which could be at neutral.

Thanks to you all. 

-leif laaksonen


>This may be of interest as an example of Web scientific
>publishing; it's like an abstract with popup color plates.
>
>        http://neuron.arc.nasa.gov/papers/spie_abstract.94/.index.html
>
>Bill Ross
>
>---Administrivia: This message is automatically appended by the mail exploder:
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From ross@cgl.ucsf.EDU  Thu Mar 17 03:42:02 1994
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From: ross@cgl.ucsf.EDU (Bill Ross )
To: Leif.Laaksonen@csc.fi, ross@cgl.ucsf.EDU
Subject: Re: CCL:Example of Web abstract with pictures
Cc: chemistry@ccl.net


	>This may be of interest as an example of Web scientific
	>publishing; it's like an abstract with popup color plates.
	>
	>        http://neuron.arc.nasa.gov/papers/spie_abstract.94/.index.html

	Making Web publications is not that simple. 

Still, for something simple, the above example is pretty darn 
impressive. Certainly, the more infrastructure, the better.
What would it take to start an electronic journal that, _purely 
on content_, all who read this email would value to the extent 
of paying something for? 

	I don't believe that one can use ordinary text and put links 
	into that. 

It's like a black-and-white movie: good info is good info & you
get it the easiest way available, and just scanning in the current
literature and automatically mapping references would be nothing
to sneeze at.

	I believe that the whole text should be written from an other 
	point of view where the links come in more logically. 

Absolutely. I don't claim that the current WWW culture, which seems 
barely months old, has even begun to ripen. The language of links is 
at the stage of early cinema. There are some excellent examples of
organized productions (easy to find, since more people's pages have
pointers to them).

	The text around the links should clearly show WHAT is behind
	the link. Other aspects like type of file behind the link, file 
	sizes and so on should also be seen from the link. We are still 
	living in a world with slow network connections, after all.

Amen. I tried playing the tetraamine movie on the Australian site,
and nothing came up after an hour of downloading. 

	This whole WWW concept is quite difficult to accept by very many because
	the way we compete each other is through the publications, more or less.
	Giving the publishing away to a neutral publisher we maintain a sort of
	neutral territory. Now when the whole business is more up to ourself
	it's difficult to find a new neutral territory which could be at neutral

So, what would it take? Would an established neutral party in the
form of, say, a commercial or society publisher have to bless it, or
could a new, for-this-purpose organization overcome this barrier?

Bill Ross


From chp1aa@surrey.ac.uk  Thu Mar 17 04:42:06 1994
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From: Mr Andrew D Allen <chp1aa@surrey.ac.uk>
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Subject: CCL: Linear systems - solution
To: chemistry@ccl.net
Date: Thu, 17 Mar 94 9:29:00 GMT
Mailer: Elm [revision: 70.85]


I have recieved a specific reason why linear systems cause problems, but it has
to do with bond angles of 180 degrees. The generally accepted solution is to
employ dummy atoms to break up the Z-matrix. Ie. to have some dummy atoms at
90 degrees to the acetylene carbons to give none linear bond angles.

Other solutions involve reordering the atoms such that angle are formed from 
non-bonded atoms. This is only possible if the non-bonded atoms are not in line
and have an angle of 180 degrees. 

Thanks to all who replied.
--
################################################################################
Structural and Computation Chemistry Group__________chp1aa@uk.ac.surrey - JANET.
Department of Chemistry_____________________________phone__+44(483)-300800-2632.
University of Surrey________________________________fax_________+44(483)-300803.
Guildford, Surrey, GU2 5XH, UK______________________fpt____________131.227.110.2
################################################################################

From h.rzepa@ic.ac.uk  Thu Mar 17 05:33:53 1994
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Date: Thu, 17 Mar 1994 08:45:13 +0000
To: CHEMISTRY@ccl.net
From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa)
Subject: Re: CCL:Example of Web abstract with pictures


Leif Laaksonen writes:

>Making Web publications is not that simple. I don't believe that one
>can use ordinary text and put links into that. I believe that the whole
>text should be written from an other point of view where the links come in
>more logically. The text around the links should clearly show WHAT is behind
>the link. Other aspects like type of file behind the link, file sizes and
>so on should also be seen from the link.

in response to:

>>This may be of interest as an example of Web scientific
>>publishing; it's like an abstract with popup color plates.
>>
>>        http://neuron.arc.nasa.gov/papers/spie_abstract.94/.index.html

Firstly, I believe that the issue  of file size has been addressed, and
hopefully will be taken on board in future releases of the protocol.
As to links, people may wish to browse through
http://www.ch.ic.ac.uk/rzepa/RSC/CC/3_03989G.html

Here, I have linked a chemical structure diagram to sounds! We
are working to develop methods of defining molecules as collections
of mapped 3D objects, and linking those to, ie scripts
which produce molecular orbitals or whatever!
If anyone has produced other such links to chemistry please tell us
all!

I should also mention that the official MIME RFC (request for
comments) Internet document will shortly be finalised at our
end, and submitted for discussion! I am still looking up some
references! With a MIME "chemical" type, we can really start
linking and processing chemistry on the webb!
[please innundate with comments AFTER the RFC is published!]



Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY;
rzepa@ic.ac.uk via Eudora 2.02, Tel:+44  71 225 8339, Fax:+44 71 589 3869.
>From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804
http://www.ch.ic.ac.uk/rzepa.html




From ifm.oos@macpost.lidac.liu.se  Thu Mar 17 08:42:05 1994
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Subject: Re: CCL:Pseudo-Jahn-Teller Effect
To: CHEMISTRY@ccl.net
From: Anton van Oosten <oos@IFM.LiU.SE>
Date: Thu, 17 Mar 94 14:35:51 +0100
Message-Id: <940317.143551.23114@macpost.lidac.liu.se>


Bill Hobey writes:

>In reply to Anton Van Oosten's question, I interpret the Jahn-Teller Effect
>as the coupling of two degenerate electronic states through a vibrational
>mode of motion, while the Pseudo-Jahn-Teller Effect is the coupling of two
>nearly degenerate electronic states through a vibration. Mathematically,
>the only difference is that the diagonal matrix elements (in, say, a
>perturbation treatment) are equal in one case, and differ to a "small"
>extent (of the order of vibrational energies) in the other. Physically,
>there appears to be no significant difference between the two cases.

There is a more important mathematical difference: the JT effect is first order 
in deformation (or vibration) and the Pseudo-JT effect second order.

But I will restate my original point more precisely. 

The JT theorem predicts that the energy of a degenerate state will always be 
lowered, in first order, by a symmetry breaking deformation. In its most general 
formulation, the theorem is derives from symmetry considerations and the 
Hellmann-Feynman theorem. 

In some cases, but not always, symmetry breaking also occurs if there is no 
degeneracy, but now in second order. Is there a Pseudo-Jahn-Teller rule that 
*predicts* whether this will occur or not ?


_____________________________________________________
Anton Van Oosten
University of Linkoeping     Internet: oos@ifm.liu.se
IFM/FOA, FOA-huset           Phone:    +46  13 282380
S-581 83 LINKOEPING SWEDEN   Fax:      +46  13 142337       
_____________________________________________________

From whobey@WPI.EDU  Thu Mar 17 11:42:08 1994
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Date: Thu, 17 Mar 1994 10:53:41 -0500
Message-Id: <199403171553.KAA05621@wpi.WPI.EDU>
To: CHEMISTRY@ccl.net
Subject: Pseudo-Jahn-Teller, again


In my last communique I confused my own references. The paper discussing the
dynamical Pseudo-Jahn-Teller Effect is

W.D.Hobey, J. Chem. Phys. 43, 2187-2199 (1965).

In the situation where the two electronic states are "nearly" degenerate, 
second order theory is inadequate to calculate the DYNAMICAL vibronic
wavefunctions. Rather, a matrix formulation should be used.
	However, Anton Van Oosten's question seems more oriented toward
a STATIC treatment of distortions. In that case, symmetry considerations
which are a direct extension of the type used for Jahn-Teller distortions
are in order. A rather extensive treatment along these lines can be found
in Chap. 3 of

R. Englman, "The Jahn-Teller Effect in Molecules and Crystals", Wiley-
Interscience, 1972.

(Other references were given in a discussion on this subject on the CCL net
in Oct. 1992).

				Bill Hobey

From jstewart@fujitsu.fai.com  Thu Mar 17 11:47:04 1994
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From: jstewart@fai.com (Dr. James Stewart)
Message-Id: <9403171619.AA01622@fujitsu.fai.com>
To: chemistry@ccl.net
Subject: MOPAC 7 and MOPAC 93


Kay Kreidler asks: 

> What are the differences between MOAPC 7.0 and MOAPC93? I thought, you can
> calculate pKa-values with MOPAC 7.0, but we got a copy by QCPE and it
> seems, that this is not true. Does anyone know, how to get MOAPC93 and
> what its price is (I think it's commercial).
>  

To reiterate:

MOPAC 7 is public domain software.
MOPAC 93 is copyrighted software.
MOPAC 7 is intended for use by software developers ONLY.
        It is NOT intented to be used in production work.
Both MOPAC 7 and MOPAC 93 can be obtained through the QCPE.
MOPAC 7 is available at the standard QCPE cost.
MOPAC 93 is available at the standard QCPE cost for non-profit organizations
(academic institutions, for example).
MOPAC 93 is available for $2,000 to profit making orgainizations.

pKa can be calculated by both MOPAC 7 and MOPAC 93.
pKa is calculated using the COSMO solvation model.



Everyone who gets MOPAC 93 must sign an end-user agreement.

James J. P. Stewart

From shenkin@still3.chem.columbia.edu  Thu Mar 17 11:49:33 1994
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From: "Peter Shenkin" <shenkin@still3.chem.columbia.edu>
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Date: Thu, 17 Mar 1994 11:41:43 -0500
In-Reply-To: apa@adfa.oz.au (Alan Arnold)
        "CCL:Legal issues about stuff put under Mosaic" (Mar 17, 11:22am)
References: <199403170122.AA11622@sserve.cc.adfa.oz.au>
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Just a few explicit examples.

First, my most recent signed copyright agreement with a journal publisher
states that the author may make and distribute copies of the work, provided
that the copyright notice remains intact.  Thus this agreement, at least, would
seem to allow electronic publishing via WWW and access via Mosaic.

Second, at a recent meeting here, an art history professor described how a book
of art reproductions is being made available to a class by this means.  In
response to a question from the audience, it turned out that special permission
had been obtained from the publisher to do this, and that distribution is
limited to Columbia.

Third, E. T. Jaynes's has made his most recent book available in TeX form by
anonymous ftp, and there are also links to it, chapter by chapter, in an http
document at SUNY Albany, as I recall.  I brought it over and printed about a
quarter of it, which forms a stack about an inch thick.  It would be much nicer
to have it in the form of a "real" book.  So I'm not so certain that electronic
publishing is going to put the paper publishers out of business.

	-P.


From toni@athe.wustl.edu  Thu Mar 17 12:42:20 1994
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From: toni@athe.wustl.edu (Toni Kazic)
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To: CHEMISTRY@ccl.net
In-Reply-To: <9403170844.AA13972@cscmgb.cc.ic.ac.uk> (h.rzepa@ic.ac.uk)
Subject: Re: electronic publishing (long)
Content-Length: 5438



I've been very interested in the discussion since it reflects some of my own experience
with the multiple sides of these issues.  Here is my current thinking, endorsed by no one
official. I'm not an attorney and I realize copyright lawyers make a living trying to sort
these issues out, so what I'm saying is really jailhouse lawyering --- but I think these
issues are too important to be left to lawyers!  My usage of such terms as "publish",
"distribute" and "paper" is variable, but I hope clear in context; rethinking
those would take a while.


It seems to me a look at current usage is advisable as we try to develop reasonable
standards.  I suggest technology is augmenting and encouraging what has historically been
common and apparently unobjectionable practice.  It is quite customary for authors to
distribute preprints and reprints of their work by paper, and no one seems to complain ---
in fact this is clearly viewed as a tool in scientific competition.  When one runs out of
reprints one xeroxes the paper and mails it.  Since most people want their reprint
immediately, they xerox the paper themselves, and my understanding is this use is
permitted under current US law.  With the growth of camera-ready copy and electronic
document preparation, the practical distinction between an "official", glossy reprint from
the publisher and a xeroxgraphic copy fades even further, particularly when photographic
plates are not involved.  Increasing use of direct image capture makes even plates moot,
and can considerably improve the quality of scientific discourse by making a better
approximation of the "real" data available (one can have difficulty with getting the color
right on the plates, or affording the page charges for such items).  Making document/data
files available on the web, gopher or by anonymous ftp is increasingly common, and I claim
that is a logical extension of xeroxing a paper and mailing it out.  (I warned you, I'm
not a lawyer ;-).)  It certainly does reproduce the appearance of the paper-published
version, but the representation of the information is different: a PostScript file is not
the same thing as a glossy reprint.  At least some scientific societies encourage this
practice for individual papers, though not necessarily collections.


In part the growth of reprints, official or not, is driven by the economics and space
requirements of subscription, but it also reflects the need to draw from multiple
disciplines or venues as we pursue our science. Searching the literature is no longer
constrained to thumbing through the indices of bound copies of journals, and reading
habits are surely more eclectic. Thus the cost of individual subscriptions is balanced
against the bother of using the library.  I guess the result is probably the net loss of
individual subscriptions.  Does anyone happen to have any data on this point?


Our current scientific publishing industry and the mutual, essential cooperation with
scientists was spawned by our predecessors' need to communicate without travel.  This
need is even more acute now, and we seem to be getting past arguing about the medium of
communication per se to the lurking and more basic issues of freedom of information, the
facilitation of high-quality communication, and the nature of intellectual property.  I
think publishers can continue to play an important role in marshaling reviewing and
editorial resources, organization of the publication, and provision of archival copies,
independent of the distribution mechanism, but to do this effectively they may have to
exploit aspects of current practice they find troubling.  Failure to do so may mean they
are bypassed altogether: many scientists already marshal resources, prepare camera-ready
copy and review papers.  Hugh Chou's and my earlier response to a request for electronic
abstract submission for the ACS grew out of my experience in soliciting, editing and
publishing papers for the equivalent of a symposium, and the obvious ways the business
could be streamlined for both the editor's and publisher's benefit with electronic tools.
(A plug: http://ibc.wustl.edu/, check the menu for ACS abstract submission demo.  Tom
Pierce will be displaying it at the ACS meeting in San Diego also, thanks Tom!)  Bypassing
publishers would entail important consequences, not just for the economics of scientific
publishing and royalty-related issues, but more fundamentally for the availability of
information.  What would the net-less do for the transitional period?


Many people have made excellent points about the form of HTML documents and I agree.  I'd
only add that with respect to multiple citations for the same paper, current abstracting
services occasionally list the same paper multiple times, usually because the state of the
authors' first names are altered or because the author list has been contracted.
Coordination of electronic distribution, archival time/date stamping and abstracting would
go a long way toward eliminating this problem.  I recently found myself citing both net
and publications in my references, and found a quandary when I realized I wanted to cite
the most current version of a database which was only foreshadowed in a published paper!



Toni Kazic


Institute for Biomedical Computing
Box 8036
Washington University School of Medicine
700 South Euclid Ave.
St. Louis MO  63110

314-362-3121
314-362-0234  (fax)

toni@athe.wustl.edu

From SBOESCH@aardvark.ucs.uoknor.edu  Thu Mar 17 14:42:12 1994
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From: <SBOESCH@aardvark.ucs.uoknor.edu>
Message-Id: <199403171904.OAA25351@www.ccl.net>
Date: Thu, 17 Mar 94 13:04 CST
Subject: where to locate nqs software for risc/6000?
To: chemistry@ccl.net
X-VMS-To: IN%"chemistry@ccl.net"


	Dear Netters,

		I was wondering if anyone might know where I could
		locate NQS software for the RISC/6000.
                It is batch queue software and we have been told
		that it is public domain software.
		please send any replies to me     
		SBOESCH@aardvark.ucs.uoknor.edu

		Thanks in advance and best regards

				Scott Boesch
				University of Oklahoma

From eslone@mason1.gmu.edu  Thu Mar 17 14:50:57 1994
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Subject: Info on Finnegan GC/MS
To: chemistry@ccl.net
Date: Thu, 17 Mar 1994 14:08:05 -0500 (EST)
From: "J. Eric Slone" <eslone@mason1.gmu.edu>
Cc: CHEMED-L%UWF.BITNET@uga.cc.uga.edu
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Dear Netters:

I am looking for information on the following piece of equipment:

	Finnegan OWA Automated GC/MS with a Tektronics 4006-1
	Terminal and a Control Data 9448 Cartridge Drive.

We have this piece of equipment but cannot get it working due to a
possible problem with the hard disk.  We are looking for help in
locating a replacement drive and software.

Also, if anyone is well versed in this piece of equipment and could
provide some assistance in making it functional, we would be grateful.

Please forward responses to eslone@mason1.gmu.edu

Thank you for your help.

Eric


________________________________________________________________________________

 J. Eric Slone                         Scientific Consulting Services
                                       Serving Government & Industry Since 1982
 Internet:   eslone@mason1.gmu.edu
 Compuserve: 73757,2776                "True science teaches, above all, to
 Fax:        (703) 751-6639             doubt, and to be ignorant."
 Voice:      (703) 461-7078                               Miguel do Unamuno
________________________________________________________________________________



From ghislain@jupiter.sun.csd.unb.ca  Thu Mar 17 15:12:27 1994
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To: CHEMISTRY@ccl.net
From: ghislain@jupiter.sun.csd.unb.ca (Ghislain Deslongchamps)
Subject: old E&S PS-390


Dear netters,
     This may sound like prehistory but here goes anyway:

A few years ago we acquired a used Evans&Sutherland PS-390 workstation /
MicroVaxII for running MacroModel 2.5.  After using the system successfully
for a few months, the hard disk of the MicroVax died and so did our hopes
for its revival.  We replaced the hard disk but it was preloaded with
Ultrix (MacroModel ran under VMS 4.5). We haven't been able to reload VMS
>from our old TK-50 tapes.

We have since bought an Indigo-XS24 running MacroModel 3.5X for
research-level molecular modelling but would like to revive the E&S PS-390
for undergraduate teaching purposes.

I guess the idea would be to somehow get VMS 4.5 to run again and to
re-load our old MacroModel.  Can anyone help?  Any other low-cost
suggestions?

Thanks

+++++++++++++++++++++++++++++++++++++++++++++++
+ Ghislain Deslongchamps, Assistant Professor +
+ Department of Chemistry                     +
+ University of New Brunswick                 +
+ Fredericton, N.B.  CANADA  E3B 5A3          +
+ e-mail:  GHISLAIN@UNB.CA                    +
+ phone:   506-453-4792    ext. 7254          +
+ FAX:     506-453-4599                       +
+++++++++++++++++++++++++++++++++++++++++++++++




From elcana@iqm.unicamp.br  Thu Mar 17 15:42:13 1994
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From: Anselmo Elcana de Oliveira <elcana@iqm.unicamp.br>
Message-Id: <199403171924.QAA09490@clio.iqm.unicamp.br>
Subject: Force field program
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Hi netters,

I am interested in programs to calculate force field of some organic compounds.
Does anyone know how to get then?

Thanks in advance.

	Anselmo Elcana

	ELCANA@IQM.UNICAMP.BR

