HDTenEightyP/NetNews huggingface dataset:
From: bioc07@otago.ac.nz
Newsgroups: bionet.xtallography
Subject: RE: P.E. Stein's current address
Date: 21 Jan 93 19:56:38 +1300
Distribution: bionet
Organization: University of Otago, Dunedin, New Zealand

In article <9301131703.ZM14361@pdb.pdb.bnl.gov>, abola@PDB.PDB.BNL.GOV (Enrique E. Abola) writes:
> On Jan 12,  2:00pm, edu%\ wrote:
>> Subject: Re: P.E. Stein's current address
.
.
.
>>
>>
>> My mailer messed up.  Let's try this again.  I'm looking for Penelope
>> Stein's (solved ovalbumin structure) current address or Martha Teeter's
>> directory of crystallographers.  Could anyone with this information please
>> forward it to me.
>>
>> Thanks-
>>
>> Darin Katz
>> University of Pennsylvania
>>
>>-- End of excerpt from edu%\
> 
> 
> -------------------------------------------------
> 
> The Protein Data Bank entry for ovalbumin can be retrieved by anonymous FTP
> from the PDB machine - pdb.pdb.bnl.gov.  The IDCODE is 1OVA. You can also
> get the entry by sending an e-mail request to fileserv@pb1.pdb.bnl.gov,
> including the following in your message
> 
> 		send pdb1ova  katz@a.chem.upenn.edu
> 
> The directory of crystallographers is also available on this machine.
> 
> 
> -- 
> ________________________________________________________________                                 
> 				 | 
> enrique e. abola                 |   BITNET:    abola1@bnl
> Protein Data Bank                |   INTERNET:  abola1@bnl.gov 
> Department of Chemistry          |   (516)-282-4383 
> Brookhaven National Laboratory   | 
> Upton NY 11973                   |
> ________________________________________________________________ 
> 
You could try pes@mrc-lmb.cam.ac.uk or the postmaster at that site.

     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %  Craig Marshall                               %
     %  ++++++++++++++++++++++++++++++++++++++++++++ %
     %  Biochemistry Department bioc07@otago.ac.nz   %
     %  University of Otago     Phone 64 3 479 7849  %	
     %  P.O. Box 56             Fax   64 3 479 7866  %	
     %  Dunedin                                      %
     %  New Zealand                                  %	
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.xtallography
Subject: Re: Which system for 3D graphics (FRODO/CHAIN/O)
Date: 27 Jan 93 12:25:22 GMT
Reply-To: doelz@urz.unibas.ch
Organization: EMBnet Switzerland [BASEL]

In article <C1I653.5LA@demon.co.uk>, James Petts <pettsj@visigoth.demon.co.uk> writes:
|> In article <1993Jan26.120945.1@ssrl01.slac.stanford.edu> ,
|> hudel@ssrl01.slac.stanford.edu writes:
|> >I am looking for comments on "which way to go" for 3d graphics.  We have
|> the
|> >option of buying:
|> 
|> I wont give answers to your specific questions at the end, but all the 
|> macromolecular xtallographers I know tend to prefer E&S for the display 
|> quality.
|> 
|>  ===> James Petts <===
|> 

James, you don't know all of them. I would suggest that anyone who wants to 
purchase a piece of hardare shall get all the systems of choice on-hand in 
demoing own data. I have seen people who were entirely satisfied with 
the 'less optimal' display, and others who went for big to buy the 
top-of-the line model from whatever vendor. Make also sure that the 
hardware you tend to buy  is still supported; I wouldn't recommend to 
buy something which is more than two years old in technology. That does
also apply for software - make sure that the product you want to use justifies
to become familiar with and is able to support the most recent applications
which might become available with the years. Another aspect is the CPU 
performance and upgradability. Last, ask your colleagues in your ultimate 
neighborhood which hard- and software they use. Nothing is worse than a 
collaborator who has the best graphics on the block but unfortunately 
uses a software/hardware combination noone else is knows how to use. Last,
do not buy a hardware/software in beta status unless you can cope with 
its challenges. 


Regards 
Reinhard 
-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 267- 2078     
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
               -----------------------------------------
From: R.L.Kingston@massey.ac.nz
Newsgroups: bionet.xtallography
Subject: Dimercury acetate synthesis anyone?
Date: 29 Jan 93 00:59:23 GMT
Reply-To: rkingsto@CC-VMS1.MASSEY.AC.NZ
Organization: Massey University, New Zealand



For the purposes of preparing heavy atom derivatives we would
like to synthesize dimercury acetate. Sprang and Fletterick
(J. Mol. Biol. (1979), 131, 523-551) report what seems to be a 
simple procedure for doing this. However the compound they prepare
is of low purity. Has anyone improved on their method, or does a 
superior synthesis exist ? Any help would be appreciated.

Thanks.

Richard Kingston  (R.L.Kingston@massey.ac.nz) 
Protein Crystallography Research - Massey University
       Palmerston North   New Zealand.
From: LOLL@BIOVAX.UCHICAGO.EDU ("GARAVITO")
Newsgroups: bionet.xtallography
Subject: Map plotting in PROTEIN
Date: 27 Jan 93 16:22:00 GMT
Distribution: bionet


	Does anyone out there have programs to create Postscript plot files 
using electron density maps calculated in Steigemann's PROTEIN package?
I hate to reinvent the wheel...
	Many thanks.

Pat Loll
University of Chicago
loll@biovax.uchicago.edu
From: pettsj@visigoth.demon.co.uk (James Petts)
Newsgroups: bionet.xtallography
Subject: Re: Which system for 3D graphics (FRODO/CHAIN/O)
Date: 28 Jan 93 07:42:35 GMT
Organization: No Affiliation
X-Xxmessage-Id: <A78D3E8C8A010855@visigoth.demon.co.uk>
X-Xxdate: Thu, 28 Jan 93 15:41:00 GMT
X-Useragent: Nuntius v1.1.1d13

In article <1993Jan27.122522.13837@comp.bioz.unibas.ch> Reinhard Doelz,
doelz@comp.bioz.unibas.ch writes:
>|> I wont give answers to your specific questions at the end, but all
the 
>|> macromolecular xtallographers I know tend to prefer E&S for the
display 
>|> quality.
>|> 
>|>  ===> James Petts <===
>|> 
>
>James, you don't know all of them.

Well spotted , Reinhard. You're on the ball today! That is why I gave no 
specific advice and just offered a piece of information that I felt was 
relevant, and stated explicitly that I was not offering advice, just an 
abservation. I would have thought that the rest of your helpful message
was 
pretty clear to most people, anyway.

 ===> James Petts <===

=========================================================================
   pettsj@visigoth.demon.co.uk (preferred), pettsj@cix.compulink.co.uk  
=========================================================================
James Petts   % visigoth has no connection with any other host in the
Middlesex, UK % domain "demon.co.uk" | PGP 2.0 KEY AVAILABLE FOR SWAP
=========================================================================
From: matte@sask.usask.ca
Newsgroups: bionet.xtallography
Subject: questions regarding program MLPHARE
Date: 23 Jan 93 22:56:20 -600
Organization: University of Saskatchewan
NNTP-Posting-Host: sask.usask.ca

I have been doing MIR calculations using the program MLPHARE from the CCP4 
program suite (V 2.1.3), and would appreciate answers to any of the following 
questions:

During these calculations, I do refinement and calculate phases on all cycles 
(say 10). I notice that some statistics relevant to the refinement are output 
at the end of cycle 9, (what the program calls the last refinement cycle), and 
again for the last phasing cycle (cycle 10).  My (simplistic) understanding of 
phase refinement is that the heavy-atom parameters are adjusted while minimiz-
ing the difference betwen FPH(obs) and FPH(calc), and then phases are 
calculated based on these new parameters.  If this is so, why are statistics 
given for the final refinement and phasing cycles seperately, and which of 
these are the ones that should be quoted for purposes of publication, etc  ? I 
have noticed that the statistics (ie. the Cullis R-factor and phasing power) 
from the last refinement cycle (given as cycle #9) are always quite a bit 
better than on the last phasing cycle (#10). The other thing is that the 
occupancy and/or temperature factor shifts for a given heavy-atom are quite a 
bit larger on the final phasing cycle than on the final refinement cycle. 
Looking at all of the previous cycles (except #10) it would seem that 
everything has converged properly. My final question is as to why it is not 
possible to output "most probable" phase values to the mtz reflection file, 
although there is a PHIPR LABOUT card in the program ?  The message I get back 
when I ask for PHIPR is that it is an invalid program label, or something 
related to that.  

Any information will be very much appreciated !

						Thanks,

						Allan Matte
`						Department of Biochemistry
						University of Saskatchewan
						matte@sask.usask.ca
Newsgroups: bionet.xtallography
Subject: graphics program 'o'
From: ez005078@MIZAR.UCDAVIS.EDU
Date: 21 Jan 93 07:45:27 GMT
Reply-To: ez005078@MIZAR.UCDAVIS.EDU
Organization: University of California, Davis

Are there any persons using the program 'o' on a SGI machine? I have 
some querries on the makefile - failure to compile. The version I'm
using was written for an EVS machine running a bsd4.3 Unix system. Seems
that I need to determine equivalent libraries, files, paths etc. If some-
one has already solved this problem & would like to share the info pl.
contact me, thanks.
            Joe Maxwell
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.population-bio
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 23 Jan 93 10:00:02 GMT
Distribution: bionet


New users of BIOSCI/bionet may want to read the "Frequently Asked
Questions" or "FAQ" sheet for BIOSCI.  The FAQ provides details on how
to participate in these forums and is available for anonymous FTP from
net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ.  It may also be
requested by sending e-mail to biosci@net.bio.net (use plain English
for your request).  The FAQ is also posted on the first of each month
to the newsgroup BIONEWS/bionet.announce immediately following the
posting of the BIOSCI information sheet.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Organization: University of Illinois at Chicago
Date: Tue, 26 Jan 1993 08:43:37 CST
From: <U56375@uicvm.uic.edu>
Newsgroups: bionet.immunology
Subject: IMMUNOLOGY OF AGING COLLABORATIONS

IMMUNOLOGY OF AGING COLLABORATIONS INVITED by a faculty member of University of
 Illinois' College of Medicine: In view of higher incidence of cancer/infection
s during aging, age-related changes the immune status (tumor kill, cytokines, N
K subsets, surface marker) of healthy subjects are monitored. Special emphasis
on Natural Killer (NK) cells. OTHER INTERESTS: Nutritional intervention - Bioch
emical events during lymphoid cell-cytokine or drug interaction - Immunology of
 skin - Immune profile during menstrual cycly. If interested, communicate by E
mail (U56375) or phone 312-996-6083 or FAX 312-996-2827.
From: hcollier@mbcr.bcm.tmc.edu (H.A. Collier)
Newsgroups: bionet.immunology
Subject: looking for antibody
Summary: anti-androgen receptor antibody
Date: 24 Jan 93 02:44:06 GMT
Distribution: bionet
Organization: Baylor College of Medicine, Houston, Tx
NNTP-Posting-Host: mbcr.bcm.tmc.edu

I am looking for an antibody to androgen receptor in rat. I have an Ab to
a segment of AR, but it was made in rat, and I need to use a rat adsorbed
secondary anti (ie, mouse) IgG Ab. 

To clear it up...I have rat anti-androgen receptor and I would like mouse
anti-androgen receptor.

Thank you and please email responses.
 
-- 
Heidi Collier                     Internet: hcollier@mbcr.bcm.tmc.edu
Dept of Otolaryngology
Baylor College of Medicine
Houston, TX  77030
From: epr@leland.Stanford.EDU (edwin rock)
Newsgroups: bionet.immunology
Subject: Re: Advice for Immunology Paper
Date: 26 Jan 93 18:52:01 GMT
Organization: DSG, Stanford University, CA 94305, USA

In article <25JAN93.14413776@wums.wustl.edu> wetsel_r@wums.wustl.edu writes:
>In a previous article, KJSHIV01@ulkyvx.louisville.edu (KEVIN JAY SHIVELY/SCC) wrote:
>>Hello,
>>	I am an undergraduate pre-med student at the University of Louisville.
>>I am currently enrolled in a graduate level immunology course.  The problem is 
>>we are to write a 10-30 page paper on some topic of interest in Immunology
>>that goes into a fair amount of depth.  I am interested if anyone out there
>>might have some ideas on a possibly good topic and maybe even a few pointers
>>on finding some really good research journals.  I am not wanting any responses
>>with offers of pre-fabricated papers....I always do my own work and do it well.
>>However, if anyone out there can help me with some good "starter" ideas it 
>>would be greatly appreciated.  Since this is my last semester and I have a 
>>very full schedule I would rather not spend hours in the library just trying
>>to come up with an idea.
>> 
>> 
>>						Thanks,
>> 
>>						Kevin Shively
>>						KJSHIV01@ulkyvx
>-----------------
>Kevin:
>
>If it were me, I'd go for superantigens myself.  It's facinating how SA's 
>skirt around the specificity of the immune system and stimulate T cells 
>that only bear a particular V-beta element.  I'd keep the discussion 
>limited to bacterial SA's as viral SA's are a bit more complex.  
>
>Start with Anal. Rev. Immunology 1991 with Kappler and Marrack.  Do a 
>medline on either one, and on superantigens (as a subject) itself.  After 
>that, there will be more than enough info to get you going...
>
>Happy searching!
>
>===========================================================================
>+  David L. Haviland, Ph.D.	     Internet:"haviland@kids.wustl.edu"   +
>+  Washington Univ. School of Med.   A.K.A : The Compiler                 +
>+  Dept. of Peds./Pulm. Box 8116     ICBM-Net : Just hit St. Louis        +
>+  400 S. Kingshighway               &-6  <- User is Brain Dead...        +
>+  St. Louis, MO  63110              FAX: 314-454-2476                    +
>+  (314) 454-6076                                                         +
>===========================================================================
>

Kevin,
	If you go with superantigens, be careful in accepting wholesale
the conclusions of Kappler & Marrack.  Although they ARE pioneers in the
field, they are also wildly speculative folks, and a number of their
conclusions are generally regarded as fantasy.  Good luck!  Edwin Rock
From: fgarbrec@POST.ITS.MCW.EDU (Frederick Garbrecht)
Newsgroups: bionet.immunology
Subject: resolution in SDS-PAGE
Date: 29 Jan 93 00:07:40 GMT
Distribution: bionet

I am trying to resolve the different isoforms of CD45 on SDS-PAGE gels,
but have had problems getting adequate resolution.  Since the isoforms all
migrate near the top of the gel (180-220 kD), couldn't I just run a low
percentage gel, say 5%, and run it for awhile after the dye front runs off
the bottom?  How about running taller gels?  Is there some kind of
gradient that might be helpful (I'm running linear 8% gels now)?  Any
comments would be appreciated.

Thanks
Fred Garbrecht
Medical college of Wisconsin
fgarbrec@post.its.mcw.edu
From: wetsel_r@wums.wustl.edu
Newsgroups: bionet.immunology
Subject: RE: Advice for Immunology Paper
Date: 25 Jan 93 14:41:37 GMT
Organization: MIT PLASMA FUSION CENTER
NNTP-Posting-Host: msnews.wustl.edu

In a previous article, KJSHIV01@ulkyvx.louisville.edu (KEVIN JAY SHIVELY/SCC) wrote:
>Hello,
>	I am an undergraduate pre-med student at the University of Louisville.
>I am currently enrolled in a graduate level immunology course.  The problem is 
>we are to write a 10-30 page paper on some topic of interest in Immunology
>that goes into a fair amount of depth.  I am interested if anyone out there
>might have some ideas on a possibly good topic and maybe even a few pointers
>on finding some really good research journals.  I am not wanting any responses
>with offers of pre-fabricated papers....I always do my own work and do it well.
>However, if anyone out there can help me with some good "starter" ideas it 
>would be greatly appreciated.  Since this is my last semester and I have a 
>very full schedule I would rather not spend hours in the library just trying
>to come up with an idea.
> 
> 
>						Thanks,
> 
>						Kevin Shively
>						KJSHIV01@ulkyvx
-----------------
Kevin:

If it were me, I'd go for superantigens myself.  It's facinating how SA's 
skirt around the specificity of the immune system and stimulate T cells 
that only bear a particular V-beta element.  I'd keep the discussion 
limited to bacterial SA's as viral SA's are a bit more complex.  

Start with Anal. Rev. Immunology 1991 with Kappler and Marrack.  Do a 
medline on either one, and on superantigens (as a subject) itself.  After 
that, there will be more than enough info to get you going...

Happy searching!

===========================================================================
+  David L. Haviland, Ph.D.	     Internet:"haviland@kids.wustl.edu"   +
+  Washington Univ. School of Med.   A.K.A : The Compiler                 +
+  Dept. of Peds./Pulm. Box 8116     ICBM-Net : Just hit St. Louis        +
+  400 S. Kingshighway               &-6  <- User is Brain Dead...        +
+  St. Louis, MO  63110              FAX: 314-454-2476                    +
+  (314) 454-6076                                                         +
===========================================================================
From: tsornas@dec5.ulb.ac.be (Thierry Sornasse)
Newsgroups: bionet.immunology
Subject: Re: Advice for Immunology Paper
Date: 25 Jan 93 14:39:09 GMT
Distribution: world
Organization: Free University Brussels  - Belgium -  Department of Molecular Biology

Hi networker,

I am a graduate student in immunology (probably PhD. in 6 months) and I would
be pleased to help you. I thing there are some "hot spot" in immunology today, I
hope you'll find something that fit your need among these proposals.

Antigen presenting cells: the immune response is often seen only at the output
level, I mean at the effector level. In fact, the triggering of the immune
response depends on the very subtil relationship between antigen presenting cells
and the T helper cells. I think there are two points that worth a closer look.
1) The role of the lymphoide dendritic cells (or dendritic leukocytes) in the
initiation of the immune response.
2) The regulation of the immune response and the immune tolerance by the
modulation of the costimulatory signal (the second signal require by the T helper
cells to be fully activated).

Gene knock down mice: the relatively new technique of the gene knock down has
allowed the production of different strains of mice deficient for a wide range of
function: interleukines or Invarient chain (linked to MHC II) or different
subunit of the immunoglobulin molecule....
This new type of material will allow the immunologist to discover the precise
role of a large set of immunological elements.

I think there are too many exciting subject in immunology to list it all.
If you do not find what you are looking for, I think that you will find a wide
range of up-to-date topics in "Immunology Today".

Good Work

Don't hesitate to ask me more details

(Forgive me for my exotic english)

Thierry Sornasse
Univesite Libre de Bruxelles
Lab. de Physiologie Animale
Elm: tsornas@dec5.ulb.ac.be
Newsgroups: bionet.immunology
From: bell@mari.acc-admin.stolaf.edu (David E Bell)
Subject: Ig variable domain cloning in phages
Organization: St. Olaf College; Northfield, MN
Date: Fri, 22 Jan 1993 15:56:22 GMT

Newsgroups: bionet.immunology
Subject: Ig phage expression
Organization: University of Aberdeen

hi there !

i'm interested to get into discussion about autoimmune disease...
(esp. the role of autoantibodies, the experimental models, that exist to
elucidate autoimmune disorders, the role of the CD4+ cells .......)

furthermore, if anybody has experience in doing an animal phage bank
of the antibody repertoire - i'm very excited to discuss about this !
my plans are to create a phage bank of the Ig's of autoimmune uveitis
patients, to screen these ab's. (epitope mapping, v-gene families, 
molecular mimicry)

thanks for any replies!!

tom pasternak
university of aberdeen
dept. of ophthalmology/immunology


Newsgroups: bionet.immunology
Organization: University of Aberdeen

Newsgroups: bionet.immunology
From: KJSHIV01@ulkyvx.louisville.edu (KEVIN JAY SHIVELY/SCC)
Subject: Advice for Immunology Paper
Date: Mon, 25 Jan 1993 06:29:40 GMT
X-News-Reader: VMS NEWS 1.11
Organization: University of Louisville

Hello,
	I am an undergraduate pre-med student at the University of Louisville.
I am currently enrolled in a graduate level immunology course.  The problem is 
we are to write a 10-30 page paper on some topic of interest in Immunology
that goes into a fair amount of depth.  I am interested if anyone out there
might have some ideas on a possibly good topic and maybe even a few pointers
on finding some really good research journals.  I am not wanting any responses
with offers of pre-fabricated papers....I always do my own work and do it well.
However, if anyone out there can help me with some good "starter" ideas it 
would be greatly appreciated.  Since this is my last semester and I have a 
very full schedule I would rather not spend hours in the library just trying
to come up with an idea.


						Thanks,

						Kevin Shively
						KJSHIV01@ulkyvx
Newsgroups: bionet.immunology
From: KJSHIV01@ulkyvx.louisville.edu (KEVIN JAY SHIVELY/SCC)
Subject: Thanks
Date: Tue, 26 Jan 1993 05:58:18 GMT
X-News-Reader: VMS NEWS 1.11
Organization: University of Louisville

Hello, 
It's
me again and I just wanted to thank everynoe for their response.  If I had the
time I would love to respond to each personally.  I was truly surprised with
the numerous direct responses and I am very impressed with the fact that there
are so many HIGH-MINDED readers out there.  You restored my faith in human 
nature and intelligence.  Once again, THANKS!!!!!


						Kevin Jay Shively




note:  If any other brainstorm ideas come to anyone, feel free to write me.  
Also, if I can ever help any of you in my fields of specialty (Chemistry,
Biochem, or Psychology) let me know.  Although I am probably not near the 
level of most of you guys, if I can, I will be more than happy to help.