HDTenEightyP/NetNews huggingface dataset:
From: gregg@Xenon.Stanford.EDU (Gregg L. Kasten)
Newsgroups: bionet.general,sci.chem
Subject: Looking for online molecular-structure databases
Date: 23 Aug 92 23:25:53 GMT
Organization: CS Department, Stanford University, California, USA

I am using MacMolecule 1.5 to display some simple molecules. In order
to enter the display data, I need to know the coordinates of each atom
in 3-space. The documenation says the information like this can be
garnered from databases like The Cambridge Structural Database. Is
this database, or any other database that might have such information,
available online? Right now, I'm looking for coordinates of ATP, AMP,
and cAMP.

Thanks for any hints,
Gregg L. Kasten
gregg@cs.stanford.edu
Newsgroups: bionet.general
From: nash@biologysx.lan.nrc.ca (John Nash)
Subject: Re: bionet.bionette or bionet.women ?
Organization: National Research Council of Canada
Date: Wed, 2 Sep 92 17:54:18 GMT

In article <5048@news.duke.edu> una@phy.duke.edu (Una Smith) writes:
>From: una@phy.duke.edu (Una Smith)
>Subject: Re: bionet.bionette or bionet.women ?
>Date: 2 Sep 92 15:09:36 GMT

>Some fuel for the fire:

>        bionet.wbs      Women in Biological Sciences
>        bionet.wi       Women's Issues

If we can massacre "methods and reagents" to "methds-reagnts" or whatever it 
ended up as, how about "bionet.women-in-biol" or "women-biolgsts".  I think 
that should convey the correct intention without it losing the intended 
focus.


cheers, John

John Nash                            | Email: Nash@biologysx.lan.nrc.ca.
Institute for Biological Sciences,	 | National Research Council of Canada,
Cell Physiology Group.				 | Ottawa, Ontario, Canada.
	   *** Disclaimer:	All opinions are mine, not NRC's! ***
Newsgroups: bionet.xtallography
From: mantolov@golum.riv.csu.edu.au (Michael Antolovich)
Subject: Re: Thanks - Structure co-ords.
Organization: Charles Sturt University - Riverina, Wagga Wagga, NSW, Australia
Date: Mon, 31 Aug 1992 00:05:25 GMT

In article <16733.9208270915@biochemistry.oxford.ac.uk> cdl@biochemistry.oxford.ac.uk (Craig Livingstone) writes:
>Many thanks to all of those who sent me the co-ordinates of 1MAD.   They will 
>be very useful to one of my co-workers as will the information about the EMBL 
>fileserver (reproduced below as I thought others may find it useful too!).
>  etc

	Yes this is very useful!   Are there similar servers for other
databases ?
					Michael

PS Anyone know anything about Inorganic Structures ?  I'm only familiar
with Cambridge....
-- 
______________________________________________________________________________
\          Michael Antolovich in Wagga Wagga, a great place to be be...      /
 \     mantolovich@golum.riv.csu.edu.au OR antolovich@zac.riv.csu.edu.au    /
  \________________________________________________________________________/
From: kengo@fl.lab.shionogi.co.jp (Kengo Kitadokoro)
Newsgroups: bionet.xtallography
Subject: MERLOT (In Japanese/Kanji)
Date: 3 Sep 92 05:12:09 GMT
Organization: Shionogi Research Lab.,Shionogi & Co.,Ltd.



Hi
 Does anybody tell about  the MERLOT,which was written
by Paula M.D.FITZGERALD,is an integrated package of 
computer programs for the determination of crystal structures
by molecular replacement.
 
 I would like to use the program of MERLOT runninig on
both Vax and Iris. And could any kind person tell the 
way to get the MERLOT?

 Many thanks to send e-mail for me.

BEST REGARDS,


Kengo Kitadokoro
   SHIONOGI RESEARCH LABORATORIES
   12-4,Sagisu 5-chome,Fukushima-ku
   Osaka 553,Japan
   Tel: 06-458-5861 ; FAX: 06-458-0987

   e-mail address : kengo@fl.lab.shionogi.co.jp
Newsgroups: bionet.xtallography
Subject: MOLSCRIPT
From: news@massey.ac.nz (USENET News System)
Date: Thu, 3 Sep 92 04:13:27 GMT
Reply-To: rkingsto@CC-VMS1.MASSEY.AC.NZ
Organization: Massey University, New Zealand


We wish to know how we can obtain the program MOLSCRIPT for the
SGI IRIS 4D. Could someone please tell us who to contact and where.

Thanks

Richard Kingston
(R.L.KINGSTON@MASSEY.AC.NZ)
 
Newsgroups: bionet.xtallography
From: mantolov@golum.riv.csu.edu.au (Michael Antolovich)
Subject: Orthoganol coordinates to Crystal ?
Organization: Charles Sturt University - Riverina, Wagga Wagga, NSW, Australia
Date: Thu, 27 Aug 1992 05:58:50 GMT

Here is a dumb question :-
	Does anyone out there have a 'easy' method of getting a molecule
in orthoganol coordinates into crystal coordinates ?  (We had a
structure which was taken from an X-ray, minimised it in Orthoganol
space and now want to get it back into the same X-ray space....  I guess
we have to keep some of the crystal coordinates to get the origin and
orientation right....  Any thoughts or experiences would be appreciated....
					Thanks,
					Michael
PS The X-ray was minimised in SHELX if that helps.  I was under the
impression that SHELX could probably build up a structure from known
bond distances and angles ?  (I'm not the crystallographer, just the
molecular modeller :-)

-- 
______________________________________________________________________________
\          Michael Antolovich in Wagga Wagga, a great place to be be...      /
 \     mantolovich@golum.riv.csu.edu.au OR antolovich@zac.riv.csu.edu.au    /
  \________________________________________________________________________/
From: starbuck@ucrmath.ucr.edu (aaron greenwood)
Newsgroups: bionet.xtallography
Subject: X-plor Version 3.0 on the IBM aix370
Date: 28 Aug 92 20:01:10 GMT
Organization: University of California, Riverside

The IBM aix370 is one of the machines on which X-plor 3.0 is unsupported.
Does anyone have information on installation procedures for the aix370?

Thank you,

Aaron J. Greenwood          email: starbuck@ucrac1.ucr.edu
McPhersons's Lab            tele:  ( 714 ) 787-3397
University of California
Riverside, Ca. 92501
From: VIEHMANN@DE.DESY.MPGHDB ("Hans Viehmann, MPG/ASMB Hamburg")
Newsgroups: bionet.xtallography
Subject: Plotting maps and models
Date: 1 Sep 92 11:33:32 GMT
Distribution: bionet
Original-To: xtal-log@uk.ac.daresbury
Content-Transfer-Encoding: 7BIT
Mime-Version: 1.0
X-Vms-To: IN%"xtal-log@daresbury.ac.uk"

Hi,

does anybody have an overview over what programs are available
for plotting electron density maps and crystallographic models,
either for UNIX or VMS machines ? I would like to get maps and
models out of 'O' or FRODO on our PostScript printer.

And how about the plotting options in 'O' ? Enhanced plotting
routines were announced for version 5.8, but is this version
going to be distributed in the forseeable future ?

Regards, Hans.
From: eric@bcserv.wustl.edu (Hugo (Eric))
Newsgroups: bionet.xtallography
Subject: Re: Atomic Co-ordinates Query
Date: 25 Aug 92 19:01:13 GMT
Organization: Washington University in Saint Louis, MO USA
NNTP-Posting-Host: bcserv.wustl.edu

cdl@biochemistry.oxford.ac.uk (Craig Livingstone) writes:


>******************************************************************************
**
>*Laboratory of Molecular Biophysics,             cdl@uk.ac.ox.bioch     *
>*Rex Richards Building, South Parks Road,        craig@uk.ac.ox.biop    *
>*Oxford.                               Phone: (0865)275369    *
>*UK.                                   Fax:   (0865)510454    *
>*OX1 3QU                                           *
>******************************************************************************
**
Mail toi both of these addresses bounced back.  I have the file and can
send it uuencoded if I have a valid address.
-- 
  Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu
  Dept. of Biochemistry and Molecular Biophysics|                
  Washington University School of Medicine      |               
  Box 8231, St. Louis, MO 63110_________________| (314) 362-3342
Newsgroups: bionet.xtallography
From: rkingsto@CC-VMS1.MASSEY.AC.NZ
Subject: MOLSCRIPT
Organization: Massey University, New Zealand
Reply-To: rkingsto@CC-VMS1.MASSEY.AC.NZ
Date: Thu, 3 Sep 1992 04:29:58 GMT
X-Posted-From: cc-vms1.massey.ac.nz
X-Posted-Through: sol.ctr.columbia.edu


We wish to know how we can obtain the program MOLSCRIPT for the
SGI IRIS 4D. Could someone please tell us who to contact and where.

Thanks

Richard Kingston
(R.L.KINGSTON@MASSEY.AC.NZ)
 
Newsgroups: bionet.population-bio
From: rogers@eagle (Bill Rogers)
Subject: World Population Demographics?
X-Newsreader: Tin 1.1 PL4
Organization: Sangamon State University
Date: Thu, 27 Aug 1992 15:44:50 GMT

Does anyone know the mean, median age of the human race at this time?
TIA,
Bill

--
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
<> Bill Rogers, Assistant Director for Academic Computing Services          <>
<>              Sangamon State University, HSB-115                          <>
<>              Springfield, Il 62794-9243     fax:217-786-7188             <>  
<> Internet:rogers@eagle.sangamon.edu        voice:217-786-7352(Mon.->Thur.)<>
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
From: klier@iscsvax.uni.edu
Newsgroups: bionet.population-bio
Subject: Re: World Population Demographics?
Date: 2 Sep 92 02:29:19 GMT
Organization: University of Northern Iowa

In article <BtnFqt.24r@news.cso.uiuc.edu>, rogers@eagle (Bill Rogers) writes:
> Does anyone know the mean, median age of the human race at this time?

Not quite that specifically, but _World Resources 1988-89_ (World
Resources Institute & UN Environment program) give the following data:


                        Percentage of the Population in Specific Age Groups
                               1960                         1990
                        0-14   15-64   65+            0-14  15-64  65+
 World                  37.O   57.7     5.3           31.9  61.9   6.2
 Africa                 43.6   53.3     3.1           45.3  51.7   3.0
 N & Central America    34.6   57.7     7.7           27.9  62.8   9.2
 [US                    31.0   59.8     9.2           22.1  65.7  12.2]
 S America              46.0   50.5     3.5           38.6  56.4   5.0
 Asia                   39.6   56.3     4.1           31.8  63.2   5.0
 Europe                 25.8   64.5     9.7           20.1  66.8  13.1
 USSR                   30.7   62.5     6.8           25.1  65.5   9.4
 Oceania                32.9   59.7     7.4           26.7  64.3   9.0
Organization: Queen's University at Kingston
Date: Tuesday, 25 Aug 1992 13:03:45 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
 <1992Aug21.005613.10403@news2.cis.umn.edu>
 <92234.085803FORSDYKE@QUCDN.QueensU.CA>
 <1992Aug21.154438.16333@news2.cis.umn.edu> <robison1.714747862@husc10>

Considering the fine-tuning of protein concentration as a proposed mechanism
of intracellular self/not-self discimination:

In article <robison1.714747862@husc10>, robison1@husc10.harvard.edu (Keith
Robison) says:
>        I would like to point out the following paper (just published):
>
>        Berg, O.G.  1992.  PNAS 89:7501-7505
>        The evolutionary selection of DNA base-pairs in gene-regulatory
>        binding sites.
>
>"The DNA base-pair sequences that serve as gene-regulatory sites have been
>selected to provide an appropriate functional binding for a particular
>protein.  In most cases, the function depends on the binding
>probability, which can be influenced both by the binding strength
>and by the abundance of the protein in the cell.  As a consequence,
>the same function can be achieved with strong binding sites and
>a small amount of protein or weak binding sites and a strong
>amount of protein.  However, increasing the protein burden will
>decrease the growth rate of the cells.  Thus, for maximal growth
>the protein levels should be as low as possible and the binding
>correspondingly strong.  On the other hand, sequences with a
>weaker binding can be formed in many more ways and are, therefore,
>more probable, and random mutations are more likely to produce them.
>Thus the selection pressure against an increased protein burden
>can be balanced against the random mutational drift in the recognition
>sequences...
>Keith Robison

   Forsdyke: Proteins have to be made and degraded and this imposes a "burden"
             in metabolic terms. The less synthesis and the less degradation
             that is going on, the less will be the burden. The final quantity
             of protein within a cell is the result of a balance between these
             two. If it wants to increase the quantity of a protein it can
             either increase the synthesis rate (burden up), or decrease the
             degradation rate (burden down). Thus the final protein quantity
             arrived at can be independent of net metabolic burden.
                Even if "burden" were one of the factors affecting the
             evolution of protein quantity within cells, the ability to
             discriminate self from not-self intracellularly would, in my
             opinion,constitute a more powerful evolutionary selective force.

             Sincerely,  Don Forsdyke
References:
             Robison, K. (1992) Bionet.immunology 825, 1304gmt
From: P_TRAVERS@UK.AC.ICRF (PAUL TRAVERS)
Newsgroups: bionet.immunology
Subject: Wanted - Kd transfectants in RMAS or T2
Date: 26 Aug 92 18:58:00 GMT
Distribution: bionet
Original-To: IMMUNO@UK.AC.DARESBURY

Dear ImmunoNetters

	Does anyone have, or know of, transfectants of H-2 Kd into RMAS
or (174xCEM)T2 or any other TAP deficient cell line?  I would like to 
assay a panel of peptides for binding to Kd.  

			Paul Travers
From: gchacko@magnus.acs.ohio-state.edu (George W Chacko)
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
Date: 30 Aug 92 01:44:42 GMT
Organization: The Ohio State University


I have some new references on this thread. I'm in the process of
reading them myself so I can't comment yet.

Science 257: 919-926
Science 257: 927-934

George
From: bchs1k@menudo.uh.edu (Edward S. Chen)
Newsgroups: bionet.announce
Subject: University of Houston Gene Server
Date: 3 Sep 92 23:50:57 GMT
Organization: University of Houston

The e-mail server for the University of Houston Gene Server is alive again.
However, the problem has not been completely diagnosed, and the server may
go down without notice.

Edward S. Chen
evolution.bchs.uh.edu


-- 
-------------------------------------------------------------------------------
 ... Take us from the dark, out where we can see ...
                                                    --- Paul McCartney
-------------------------------------------------------------------------------
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.announce
Subject: CALL FOR DISCUSSION: bionet.carotenoids
Date: 2 Sep 92 20:10:49 GMT
Distribution: bionet
Organization: GenBank Online Service

We have received a proposal for another new newsgroup:

bionet.carotenoids (e-mail address: CAROTENO).

Discussion will now be open through 13 September on
BIOFORUM/bionet.general (*not* on BIONEWS/bionet.announce).

Please do not post one-line messages saying only "I am in favor of
such a newsgroup".  We will collect votes later.  The discussion
period is an opportunity for anyone to bring up reservations about the
proposed charter and to propose modifications prior to the vote.  The
discussion leader may submit a revised proposal in light of the
discussion, and the new charter would be included in the call for votes
which will go out on September 14th.

Please be aware that only one vote is counted per e-mail address, so
it is necessary to have your own account in order to vote.  Multiple
votes from the same address are not accepted.  If you are interested
in the following newsgroup, but do not have an e-mail address of your
own, please obtain one from your computer center before the call for
votes is issued.

----------------------------------------------------------------------

Proposal to establish bionet.carotenoids

Discussion leader: Pablo A. Scolnik (scolnipa@esvax.dnet.dupont.com)


Purpose: discussions regarding the chemistry, biochemistry, genetics,
metabolism, and health effects of carotenoids.  This newsgroup will
also include information exchange regarding pure compounds, mutants,
techniques, and recombinant DNA constructs.

------------------------------------------------------------------
From: whide@emu.imgen.bcm.tmc.edu (Winston Hide)
Newsgroups: bionet.announce
Subject: Echinoderm Newsletter
Keywords: Echinoderm, newsletter,forum
Date: 2 Sep 92 23:00:39 GMT
Reply-To: whide@mbcr.bcm.tmc.edu (Winston Hide)
Organization: Baylor College of Medicine


  			      STARNET

This is to announce the launching of a new electronic newsletter,

			      STARNET


that is aimed at all biologists with an interest in ECHINODERMS.

The newsletter will contain information on echinoderm biologists,
want-ads, submissions from interested people and other sundry light and
also scientific fare.

If you would like to be added to the distribution list, please 
email to 

Win Hide
at

	whide@mbcr.bcm.tmc.edu


Replies for (trial?) subscription to STARNET via to bionet.announce will not be answered
as reliably as direct replies to my account. 


Win Hide
Institute of Molecular Genetics
Baylor College of Medicine

{NOTE added by moderator - this message has a Reply-To: line in its
header so that replies should be directed automatically back to WIn
instead of to the newsgroup.  I can not get into the business of
forwarding replies to messages. - DK]
From: clsmith@ux5.lbl.gov (cassandra smith)
Newsgroups: bionet.announce
Subject: New name needed for bionet.bionette?
Date: 3 Sep 92 00:45:02 GMT
Reply-To: clsmith@ux5.lbl.gov


   [Preface added by moderator (D. Kristofferson) - this newsgroup has
    already been approved for creation and we are trying to accomodate
    belated objections to the name.  It is not being put out for further
    voting or protracted discussion.  Please send your replies to the
    following in private to Cassandra Smith.]

Several scientists have raised objections to the name bionet.bionette.
Thus, we would like to solicit alternative name possibilities.
Alternative names that have been proposed thus far include (I have
eliminated "womens-issues" which is too broad):

.bionette 
.herbionet
.biowomen
.wbs       women-in-biological-sciences
.women-in-bio
.women-bio
.womens-bionet
.women


Proposed names must be limited to 14 characters on USENET segment
names.  The final suggestion should either fit the format
"bionet.xxxxxxxxxxxxxx" or break it up into
bionet.xxxxxxxxxxxxxx.yyyyyyyyyyyyyy where the x's should preferably
be one of the existing subhierarchies such as "molbio", etc.

It is important that the name, in some way, reflect the purpose of the
newsgroup.  The charter of the newsgroup is:

----------------------------------------------------------------------
The purpose of this discussion group will be to promote networking
among professional women in the biological sciences. In essence what
is proposed is a bioscience new girl network.  A major problem that
women in science face is isolation. Thus, the goal of this newsgroup
is to provide a forum where women in the biological sciences can (1)
share experiences and interests and (2) provide advice and support to
encourage women, despite obvious and not so obvious obstacles, to
enter and continue scientific careers.
----------------------------------------------------------------------


Please send suggestions to me no later than 8 September 1992.


Sincerely yours,

Cassandra Smith
clsmith@ux5.lbl.gov
From: POSTMAST@GUNBRF.BITNET
Newsgroups: bionet.announce
Subject: Announcement of PIR Network Request Server Downtime
Date: 3 Sep 92 17:47:24 GMT


            Announcement of Temporary Interruption of Access to
                   The Protein Identification Resource

The National Biomedical Research Foundation will be attempting to upgrade
software beginning on Monday 7 September.  From 9:00 EDT Monday 7 September
through about 12:00 EDT Tuesday 8 September it will not be possible for users
to access the Protein Identification Resource Network Server.  In addition
there may be a short interruption of the On-line System during that period.

Please, do not send requests to FILESERV@GUNBRF from 7 September through 8
September.  We regret any inconvenience this temporary loss of service will
cause.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER@GUNBRF.BITNET
From: kristoff@GENBANK.BIO.NET (David Kristofferson)
Newsgroups: bionet.announce
Subject: BIOSCI Newsgroups - Changes
Date: 1 Sep 92 08:00:02 GMT
Distribution: bionet



		       *** IMPORTANT NOTICE ***


After September 29th, the end of the five year GenBank Contract to
IntelliGenetics, the BIOSCI node at GenBank/IntelliGenetics will be
changed from the computer genbank.bio.net to net.bio.net.

Kenton Hoover and I will continue to run the BIOSCI node at
IntelliGenetics in the post-GenBank period.  Alan Bleasby, Steve
Marshall, Paul Griffiths and David Hines at SERC Daresbury Laboratory
will continue to serve their BIOSCI user community.

Messages sent to genbank.bio.net will be automatically received by
net.bio.net, so this transition should occur transparently to our
users.  The October version of the info sheet will have all posting
and other BIOSCI addresses changed from xxxxxx@genbank.bio.net to
xxxxxx@net.bio.net.

To repeat, the genbank.bio.net addresses will continue to function,
but people should begin adjusting their habits to utilize the new
hostname net.bio.net.  "Old hands" will recognize net.bio.net from
BIONET days; the address has the virtue of being reachable from any
site in the world regardless of the ordering convention used for host
names.

David Kristofferson
BIOSCI/bionet Manager