From owner-chemistry@ccl.net  Wed Jul 19 02:10:44 1995
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Subject: Chem-X for Windows
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Dear Colleagues;

     I would appreciate hearing from people who use (or have used) Chem-X for
Windows, particularly with respect to how they feel that the programme performs
relative to other similar programmes that are available.

     Thanks in advance to all responders.


Sincerely,

S. Shapiro
ZH, CH
toukie@zui.unizh.ch

From owner-chemistry@ccl.net  Wed Jul 19 02:40:47 1995
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Date: Wed, 19 Jul 95 02:18:47 PDT
From: Scott William Chinn <us005755@interramp.com>
Subject: 2D to 3D structure conversion
To: chemistry@ccl.net
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I understand that programs such as CONCORD, CORINA and CHEM-X
can convert 2D structures to 3D. 

I have a number of 2D structures which I would like to 
convert to 3D and then store in a relational database.

Is this possible? What does the 3D data look like? I have heard
that CHEM-X will give you something like 400 bitwise operators, which
somehow describe the 3D stucture. Is this correct?

Any comments would be most helpful.

THANKS!
Scott


Name: Scott William Chinn
E-mail: us005755@pop3.interramp.com (Scott William Chinn)



From owner-chemistry@ccl.net  Wed Jul 19 03:40:54 1995
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From: michaels@jake.chem.unsw.EDU.AU (Michael Shephard)
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Subject: Compiling Mopac93 on an SGI Summary
To: chemistry@ccl.net
Date: Wed, 19 Jul 95 17:32:22 PDT
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****************
Original Post
****************
I am having difficulty in compiling Mopac93 (Release 2 obtained
from QCPE) for an SGI machine (R4400 Indigo Irix 5.2)

Well, actually it compiles OK without error but the mopac.exe
produced doesn't work very well at all.

Is there am SGI version of the source, or is the sun source supplied
the "generic unix version", or possibly there is an SGI version of the
makefile?

****************


The replies I recieved can be basically summarized as:
"We had no problem in compiling Mopac93 for an SGI although
the supplied job submission script, mopac.csh, is a dud."
followed by an offer of help.

Thanks to:
Georg Ostertag
Satyam
Steve Bowlus
Walter E. Reiher III

However, Steve Bowlus and Walter E. Reiher III noted that it may
be the flags supplied to the compiler that may be causing the problems
and on examining extracts of their makefiles, this proved to be the case.

The key compiler option missing from the Mopac93R2 makefile was the
"-static" flag.

The modifications to the makefile (as given by Walter E. Reiher III)
are:

Note that the "SPARC" flags have been modified so
they are now "SGI" flags. It would be more elegant
to add a seperate SGI section to the makefile so
it can both 'make sgi' and 'make sparc'.

************************
Modified Makefile flags
(a "-mips2" flag can be added to SPARCFFLAGS
depending on the SGI machine mopac is
being compiled for)
************************

SPARCFC           = f77
SPARCFFLAGS       = -O -static -Olimit 1350
SPARCCPP          = do_cpp_sgi.csh
SPARCEXE          = ../mopac.exe
SPARCEXTRAS     = blas.o

**********************
do_cpp_sgi.csh script
(place in the mopac_sun_source directory)
**********************

#!/bin/csh -f
#
#       DO_CPP_SGI.csh
#       Run the C preprocessor on SGI
#
#  WER
#  Tue Feb 22 13:45:50 PST 1994
#
#
f77 -P $1 
mv `basename $1 .f`.i $2

****************************

--
_________________________________________________________________________
| Michael Shephard.                  |      M.Shephard@unsw.EDU.AU      |
| University of New South Wales.     |  michaels@jake.chem.unsw.EDU.AU  |
| Australia                          |                                  |


From owner-chemistry@ccl.net  Wed Jul 19 07:40:52 1995
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From: "G. Ravishanker" <ravishan@swan.wcc.wesleyan.edu>
To: chemistry@ccl.net
Subject: Color Flatbed Scanners



Hi

	We are looking into purchasing a color flatbed scanner, presumably
one that can hook upto either a PC or a Mac (A network one would be even
better...) to scan color figures (8.5" X 11") in regular paper,
transparencies and more importantly color slides. If you have any
suggestions, please send them to me. Thanks in advance.

Ravi

From owner-chemistry@ccl.net  Wed Jul 19 08:25:49 1995
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To: chemistry@ccl.net
From: pis_diez@nahuel.biol.unlp.edu.ar (Reinaldo Pis Diez)
Subject: Book on Parallel Programming 


        Hi netters,

                I dont have experience in parallel programming in Fortran
but I'm interested in learning about it. Any references about books on the
subject will be welcome.

                Send answers to me please. I'll summarize to the net.

                Thanks in advance,

                
                                                                            
                            Reinaldo


From owner-chemistry@ccl.net  Wed Jul 19 09:40:52 1995
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Date: Wed, 19 Jul 95 09:48:33 -0400
From: polowin@hyper.hyper.com (Joel Polowin)
Message-Id: <9507191348.AA02893@hyper.hyper.com>
To: Scott William Chinn <us005755@interramp.com>
Subject: Re:  CCL:2D to 3D structure conversion
Cc: chemistry@ccl.net


> Date: Wed, 19 Jul 95 02:18:47 PDT
> From: Scott William Chinn <us005755@interramp.com>
> Subject: CCL:2D to 3D structure conversion
> 
> I understand that programs such as CONCORD, CORINA and CHEM-X
> can convert 2D structures to 3D. 
> 
> I have a number of 2D structures which I would like to 
> convert to 3D and then store in a relational database.
> 
> Is this possible? What does the 3D data look like? I have heard
> that CHEM-X will give you something like 400 bitwise operators, which
> somehow describe the 3D stucture. Is this correct?

Conversion from 2D to 3D is a function offered by several packages
(including ours).  Basically, a set of relatively simple rules is used
to generate 3D geometry, using standard bond lengths and angles.  The big
problem is that the 2D structure is usually quite different from the
desired 3D result; often the 2D structure doesn't have a lot of cues for
stereochemistry or overall conformation.  You should check the results
of such an automated conversion before using them.  (After all, even in
doing a 3D structural optimization by standard methods one sometimes
finds a local minimum that is, by the standards of an intelligent chemist,
obviously a poor structure.  A 2D --> 3D structure conversion is a still
cruder operation.)

I don't know relational databases.  When HyperChem does a 2D --> 3D
conversion, what comes out is a 3D structure: each atom has 3D coordinates
and a set of bonds to other atoms.

Regards,
Joel
 
------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: polowin@hyper.com 

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: info@hyper.com    Support questions to: support@hyper.com
Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com
WWW: http://www.hyper.com/



From owner-chemistry@ccl.net  Wed Jul 19 09:55:50 1995
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Date: Wed, 19 Jul 1995 09:34:29 -0400 (EDT)
From: "Bruce W. Church" <brucec@arthur.bio.cornell.edu>
To: CHEMISTRY@ccl.net
Subject: Rasmol 2.5 and Tk 4.0 
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Hi
        Has anyone managed to get interproccess communication using 
Tk4.0 to work with RasMol 2.5.1 via the send command?  Send works 
fine with Tk3.6 but RasMol does not even show up as a registered interpreter
when Tk4.0 is running. 

I'm not on the list so please respond to my email address. 


Thanks in advance,

        Bruce Church
        bwc1@cornell.edu



From owner-chemistry@ccl.net  Wed Jul 19 09:55:53 1995
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From: frisch@lorentzian.com (Mike Frisch)
Message-Id: <9507191341.AA17356@mjf>
Subject: Re: CCL:G94 warning against LANL1DZ
To: chemistry@ccl.net
Date: Wed, 19 Jul 1995 09:41:27 -0400 (EDT)
In-Reply-To: <199507182056.PAA35571@audumla.students.wisc.edu> from "" at Jul 18, 95 03:56:52 pm
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Eric V. Patterson writes:
> 
> Dear Netters-
>         In the G94 User's Reference (pg. 23), a small footnote warns that
> the use of LANL1DZ is "strongly discouraged".  Can someone tell me why? 
> The best I can tell, LANL1DZ and LANL2DZ only differ in the use of D95V for
> the former and D95 for the latter on first row atoms.  Is there some
> general flaw with LANL1DZ that I should be aware of?  Any help is
> appreciated.
> 
> Eric
> 

LAN2 and LAN1 differ in how many electrons are replaced by the ECP for
some elements (near the right in each row of transition metals):  LANL2
includes the next lower s and p electrons in the valence (i.e., does
not replace them with the core potential) and this produces considerably
better reliability.  The note about discouraging LANL1 is at the request
of Jeff Hay; refer to his original papers on these potentials for details.

Mike Frisch

From owner-chemistry@ccl.net  Wed Jul 19 09:57:42 1995
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From: toni@athe.wustl.edu (Toni Kazic)
Message-Id: <9507191344.AA03740@athe.wustl.edu>
To: us005755@interramp.com
Cc: chemistry@ccl.net
In-Reply-To: <Chameleon.4.01.2.950719023125.us005755@.interramp.com> (message from Scott William Chinn on Wed, 19 Jul 95 02:18:47 PDT)
Subject: Re: CCL:2D to 3D structure conversion


Scott,

It is certainly possible.  I have some experience with CONCORD, having used
it to convert isomeric SMILES strings to pdb files (there are more choices
of input and output formats).  The pdb files produced contain the smiles
string, the Cartesian coordinates, and a connection table, and can easily
be read by humans or other programs.  You can view several hundred at
http://ibc.wustl.edu/klotho/.  If your SMILES string doesn't specify the
stereochemistry, CONCORD will try and choose for you.  The structures it
gets usually accord pretty well with both chemical intuition and crystal
structure (see J. Chem. Info CS 33:155-163, 1993), though it does have
limitations and does sometimes produce a howler.  I have no experience with
Corina yet, but from what I hear and read its strengths are complementary
to CONCORD's weaknesses and would be a good alternative (please let's not
have a flame war).  They now have a free email server, and I'm planning to
try it out (it's been reported on this list just recently).  I have no
experience with ChemX.  The hardest part may be generating the input for
the conversion program; if you think Klotho would be of some assistance to
you please let me know.



You may be able to find coordinates for your molecules.  For example the
NCI has its files up on a gopher server, though last time I looked there
was no easy way of retrieving a specific molecule.  Try the NIH web site, I
think there is a pointer from there (sorry I am unable just now to give you
the complete address).  Data from Cambridge Crystallographic Database are
proprietary.  I know a number of software vendors sell databases of small
molecules in various forms, usually bundled with their software.



You may want to give some thought to the types of queries you wish to run:
this has a significant impact on choice of database model, organization of
the database, and representation of the data.


Good luck,

Toni Kazic
Institute for Biomedical Computing
Washington University

From owner-chemistry@ccl.net  Wed Jul 19 10:25:56 1995
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Date: Wed, 19 Jul 95 10:23:24 EDT
From: Luke Anthony Burke <burke@crab.rutgers.edu>
To: chemistry@ccl.net
Subject: rotational spec
Message-ID: <CMM-RU.1.4.806163804.burke@crab.rutgers.edu>


Dear CCLers:
	Would anyone know of any programs (for any platform) that calculate
the rotational eigenvector-eigenvalue problem for any type of molecule?

Please send responses (and requests to share the responses) directly to my
e-mail address.
Thanks in advance,

Luke Anthony Burke              tel:609-225-6158
Department of Chemistry	        fax:609-225-6506
Rutgers University              e-mail:
Camden, NJ 08102                burke@camden.rutgers.edu
USA

From owner-chemistry@ccl.net Wed Jul 19 09:41:32 1995
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Date: Wed, 19 Jul 1995 09:34:29 -0400 (EDT)
From: "Bruce W. Church" <brucec@arthur.bio.cornell.edu>
To: CHEMISTRY@ccl.net
Subject: Rasmol 2.5 and Tk 4.0 
Message-ID: <Pine.A32.3.91.950719092809.20993F-100000@arthur.bio.cornell.edu>




Hi
        Has anyone managed to get interproccess communication using 
Tk4.0 to work with RasMol 2.5.1 via the send command?  Send works 
fine with Tk3.6 but RasMol does not even show up as a registered interpreter
when Tk4.0 is running. 

I'm not on the list so please respond to my email address. 


Thanks in advance,

        Bruce Church
        bwc1@cornell.edu




From owner-chemistry@ccl.net  Wed Jul 19 11:55:54 1995
Received:  for jkl@ccl.net
	by www.ccl.net (8.6.10/930601.1506) id LAA08885; Wed, 19 Jul 1995 11:47:51 -0400
Date: Wed, 19 Jul 1995 11:47:51 -0400
From: Jan Labanowski <jkl@ccl.net>
Message-Id: <199507191547.LAA08885@www.ccl.net>
To: chemistry@ccl.net
Subject: Add: Protein Adviser - Viewing, Analysis, Drawing
Cc: jkl@ccl.net


And another one:

Protein Adviser - A Biomolecular Structure Viewer, Analysis and Drawing Software

Protein Adviser is a tool to visualize, analyze and draw biomolecular 
structures. It allows for easy manipulation of all entries in the Protein 
Data Bank: Proteins, DNA and compounds bound to them. The program provides:

1. Structure Viewing - animation and stereo views, alpha-carbon trace, etc.
2. Distance based Structure Picking
3. Sequence based Structure Manipulation 
4. 3D Structure Comparison - extracting of common substructures.
5. 3D Structure Drawing - coloring and labeling of residues, bases and compounds
that can be easily moved to other Macintosh DTP software with copy and paste. 
6. Other features include: Id Code Search for specified structures from 
Brookhaven Protein Data Bank, and Output in forms of PostScript, PICT and PDB.

Protein Adviser runs on Macintosh computers with System 7 or later with 5MB RAM.

Computer Chemistry Section
Fujitsu Kyushu System Engineering LTD
Hakata Eki Mae 1-5-1, Hakata-ku, Fukuoka 812, Japan
TEL: +81-92-472-0714; Fax: +81-92-483-0663
E-mail: ccs@fqs.fujitsu.co.jp
 



From owner-chemistry@ccl.net  Wed Jul 19 11:57:34 1995
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Date: Wed, 19 Jul 1995 11:45:51 -0400
From: Jan Labanowski <jkl@ccl.net>
Message-Id: <199507191545.LAA08846@www.ccl.net>
To: Chemistry@ccl.net
Subject: Add: LiqCryst - Dbase of Liquid Crystal Compounds
Cc: jkl@ccl.net


I was asked to post this short add:

LiqCryst - Database of Liquid Crystalline Compounds for Personal Computers
(by Volkmar Vill, Institute of Organic Chemistry, University of Hamburg)

     LiqCryst is an integrated system of data and functions.  LiqCryst contains
the knowledge about all thermotropic liquid crystals. More than 60 000 structu-
res are extracted and carefully  checked from more than 10 000 references. 
Included are calamitics, discotics, polymers, surfactants, and lipids. Compiled 
for all compounds are phase schemes,  transition temperatures, elastic
constants,  spontaneous polarizations, indications to spectroscopy, etc.
Sources: journals, books, patent literature, conference proceedings and PhD 
theses. The program  allows quick  search  for substructures, similarity, 
chemical elements, phase sequences,  transition temperatures,  physical 
measurements and references.   Compounds are displayed in tables. Homologous 
series can be expressed in a graph.  LiqCryst allows very simple statistical
analysis of structure-property-relationship and prediction of transition 
temperatures of  new compounds by statistical  extrapolation from the data of 
known similar compounds. System Requirements: IBM-compatible PC (386+), 600 kB 
free RA and about 15 MB disc space. 
Distribution and further information available from: 
                         Fujitsu Kyushu System (FQS), 
                         Computer Chemistry Section
                         Hakata Eki Mae 1-5-1, Hakata-ku, Fukuoka 812, Japan
                         TEL: +[81] (92) 472 0714 


From owner-chemistry@ccl.net  Wed Jul 19 13:40:55 1995
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To: chemistry@ccl.net
From: "Sergei Vyboishchikov"  <SERGEI@ps1515.chemie.uni-marburg.de>
Date:         19 Jul 95 19:28:04 MDT
Subject:      Literature on Coupled Cluster Wanted
Return-Receipt-To: "Sergei Vyboishchikov"  <SERGEI@ps1515.chemie.uni-marburg.de>
Priority: normal
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Message-Id: <21A8F8F51A8@ps1515.chemie.uni-marburg.de>


Dear Netters,

I am looking for reviews concerning Coupled Cluster methods and
Quadratic Configuration Interaction methods.

Let me thank you in advance.
                                  Sergei Vyboishchikov
                                  Universitaet Marburg

From owner-chemistry@ccl.net  Wed Jul 19 13:55:56 1995
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Message-Id: <9507191040.ZM3668@herzberg>
Date: Wed, 19 Jul 1995 10:40:56 -0700
In-Reply-To: "Bruce W. Church" <brucec@arthur.bio.cornell.edu>
        "CCL:Rasmol 2.5 and Tk 4.0" (Jul 19,  9:34am)
References: <Pine.A32.3.91.950719092809.20993F-100000@arthur.bio.cornell.edu>
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
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Subject: Re: CCL:Rasmol 2.5 and Tk 4.0
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On Jul 19,  9:34am, Bruce W. Church wrote:
> Hi
>         Has anyone managed to get interproccess communication using
> Tk4.0 to work with RasMol 2.5.1 via the send command?  Send works
> fine with Tk3.6 but RasMol does not even show up as a registered interpreter
> when Tk4.0 is running.
>-- End of excerpt from Bruce W. Church

Wow, nasty. I was just looking at the source. Rasmol does not use libtk, it
uses a home-made way of interfacing with Tk's "send" command. I imagine that
rasmol doesn't work with Tk4.0 because how send works has changed in some
subtle way.  Someone might be able to enlighten us. Software engineering has
its place!



-- 

---------------------------------------------------------
Ernest Friedman-Hill
Senior Member of Technical Staff
Scientific Computing Department
Sandia National Laboratories
Org. 8117, MS 9214
PO Box 969 Livermore, CA 94550


From owner-chemistry@ccl.net  Wed Jul 19 14:25:57 1995
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Date: Wed, 19 Jul 95 14:12:19 EDT
From: dychen@nmr400.bgsu.edu (D. Y. Chen)
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To: chemistry@ccl.net
Subject: msi packages



hello everyone,
as i understand, our university is on an evaluation process for the package(s)
licensed to msi (molecular simulations inc.), there are quanta, charm, x-plor,
nmr compass and nmrpipe... i'd like to hear from people who have experience on
these packages. any feedback, good or bad, will help us to evaluate this deal.
i was also told nmrpipe is free distributed and would like to know more about 
obtaining one copy of it. many thanks!!                                   chen

(as usual, i will summarize the responses if people are interested.)

