HDTenEightyP/NetNews huggingface dataset:
From: strom@u.washington.edu (Mark S. Strom)
Newsgroups: bionet.software
Subject: Macaw and saving color screen output
Keywords: macaw, screen dumps, slides, color transparencies
Date: 28 Jul 92 16:22:45 GMT
Organization: Bifunctional Enzyme Lab, Dept. Microbiology, U.W.

There's been a number of articles posted recently on Macaw, but none seem to 
touch on the problem described below.

I've recently tried out Macaw 1.05 using Windows 3.1 for sequence alignment 
of several related proteins.  I really like the color schematic and 
alignments it gives-in fact, I like it so much I want to make 
color slides/transparencies of a set for a presentation.  However, this 
doesn't seem to be easily done.  The only way to export a file (that I can 
see) is as a text file.  Does anyone know how the screen output could be 
imported into a graphics program such as Harvard Graphics?  I know there 
are commercial screen capture programs for Windows that might do this, but 
I'm a little short of cash right now  8^). 

I have written to Greg Schuler at NCBI for the manual, and maybe this is 
explained in there, but I thought I'd give this newsgroup a shot too.  
Thanks to all who may be able to help. 

Mark
-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Mark Strom                                phone     (206) 543-4318
Department of Microbiology SC-42          fax       (206) 543-8297
University of Washington                  email     strom@u.washington.edu
Seattle, Washington 98195
From: FORNACE@FCRFV2.NCIFCRF.GOV
Newsgroups: bionet.software
Subject: Re: Reference Managing Program
Date: 24 Jul 92 16:03:38 GMT
Distribution: bionet

In article <1992Jul20.050024.20242@gserv1.dl.ac.uk>, BIONET@EARN.FRCGM51 writes:
>         Has anyone heard of an apparently similar package called "Reference
> Manager" from RIS (Research Information Systems) ?
>
> ***************************************************************************
> J-L. Risler                             risler@frcgm51.bitnet


I'm surprised no one has suggested Bookends which is a hypercard
program for the Mac that does just about everything that
the other programs do for less $$.  It will also handle 
very large stacks of >> 1000 references and will import
from Medline etc. and export in any reference format that
you wish.

Al Fornace
From: MURPHY@UK.AC.AFRC.JII
Newsgroups: bionet.software
Subject: Re: Macaw/ saving screen output
Date: 29 Jul 92 09:15:00 GMT
Distribution: bionet
Original-To: BIO-SOFTWARE@UK.AC.DARESBURY

With Windows 3.1 you can capture the screen to the Clipboard by PrintScreen
(or occasionally Shift+PrintScreen or Alt+PrintScreen). You can then paste it
back into Harvard Graphics or Freelance. However, its a bitmap and in my
limited experience weird things happen to the resolution and colours. Is there
a better way?
Cheers
From: kumar@neb.com (Sanjay Kumar)
Newsgroups: bionet.software
Subject: Molecular graphics software for Sun system ?
Date: 31 Jul 92 14:03:48 GMT
Distribution: bionet


Sorry if this is a FAQ....

What software is available for viewing structures 
encoded in PDB files on a SUN Sparcstation?

Thaks in advance.

Sanjay Kumar
New England Biolabs
kumar@neb.com
From: miski@KODAKI.KODAK.COM (Mahmut Miski)
Newsgroups: bionet.software
Subject: Re: Molecular Graphics on PCs
Date: 22 Jul 92 14:08:59 GMT
Reply-To: miski@kodaki.kodak.com
Distribution: bionet


I use "Alchemy III" and "PCModel, v. 4.0" on my Mac. In addition to
its native format, Alchemy (from Tripos Associates, Inc.) can read
and write MM2, Sybyl formats but only able to read PDB and X-ray
crystallographic data. Alchemy offers real-time animation during
wire-frame display mode, also able to display space filling (CPK),
cylinder and ball-stick models in both mono and stereoscopic form. The  
graphical output (to screen and printer) of Alchemy is superior to the
PCModel. However, molecular dynamic calculations (energy minimization) of
PCModel appears to be more reliable than Alchemy. K. Gilbert's PCModel can
read and write MM2, Macromodel, MOPAC, X-ray crystallographic data, Sybyl,
Chem-3D and PCM formats. Both packages are commercial, however, they offer
substantial discounts to the academic users.

I believe these packages might handle small to mid-size molecules properly,
however, for proper handling of large molecules (i.e., proteins) one might 
need faster machines (Mac Quadra line or 486 DOS Machines) as well as a lot 
of RAM's on the board. Nevertheless, even under these conditions performance
of these programs will not be close to those high end molecular graphics
packages running on workstations with a dedicated high resolution monitor.  

M. Miski                                      Miski@kodak.com
Sterling Winthrop Pharmaceuticals R & D
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453)
Newsgroups: bionet.software
Subject: Re: Macaw
Date: 23 Jul 92 16:20:00 GMT
Distribution: bionet


Paul Furbacher writes :

>Has the multiple sequence alignment program called MACAW (for
>Windows) been updated from version 1.0?  (....) 
>If it has been updated, where is it available? (....) 

You can obtain Macaw 1.05 by anonymous ftp from ncbi.nlm.nih.gov
in the /pub/macaw directory.

Sincerely,

Dan Jacobson
From: BIONET@EARN.FRCGM51
Newsgroups: bionet.software
Subject: Molecular Graphics on PCs
Date: 21 Jul 92 17:56:00 GMT
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: IN%"bio-software@daresbury.ac.uk"


 
        Like many others, I'm amazed by the performance/price ratios of the
i486-based PCs. Three years ago, I was a fan of the Macintosh and
considered the PCs with some condescencion. Now I'm changing my mind. Even
the monstruous MS-Windows is quite fast!
 
        Well, we need here a graphics system to *visualize* protein
structures. Not edit them and perform huge calculations. Just visualize in
a comfortable environment. We thought of a SGI Indigo machine. But now...
 
        Does anyone know a good molecular graphics package for the PC,
running -for example- under MS-Windows or SCO Unix (X-Windows) ? Can be
commercial if necessary.
 
        Thank you.
 
---
J-L. Risler                                     Bionet@frcgm51.bitnet
Centre de Genetique Moleculaire                 Risler@frcgm51.bitnet
91190 Gif sur Yvette   France
From: BIONET@EARN.FRCGM51
Newsgroups: bionet.software
Subject: Graphics on PCs
Date: 22 Jul 92 18:36:00 GMT
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: IN%"bio-software@daresbury.ac.uk"


 
        Following my request for a molecular graphics package for PCs, I've
received some answers (my thanks to Harry Mangalam) that directed me to
HyperChem. I FTP'ed the demo from D. Gilbert's server. The file name is
Hyprchem-demo.zip
        I therefore assume that it is a Zip-encoded file. Well, how do I
de-zip it ? Please excuse my stupidity.
 
        As regards R. Doelz's reply about molecular graphics:
 
1) I don't understand the "eight bits" point. As far as I know, the i486
   machines are genuine 32 bits computers ?
2) The price is not as high as stated. We've bought last week the following
   clone:
        * i486-DX2 processor @ 50MHz with coprocessor
        * 8 Mb RAM
        * 5"1/4 and 3"1/2 floppy units
        * 250 Mb hard disk
        * 17" high resolution color monitor (1280x1024)
        * MS-Dos 5, MS-Windows 3.1 and mouse
 
        for 27,000 FF (approximately $ 5,000)
 
        Here in France, we need at least three times this amount to get the
basic minimal configuration of an SGI Indigo ... which, admittedly, is not
a PC and has tremendous graphics capabilities if not basic and minimal.
 
        Well, in any case, I hope to be able to run the HyperChem demo on
that machine. I'll post the results on the net.
 
---
J-L. Risler                                     Bionet@frcgm51.bitnet
Centre de Genetique Moleculaire                 Risler@frcgm51.bitnet
91190 Gif sur Yvette   France
From: ech5w@milton.u.washington.edu (E Chris Holman)
Newsgroups: bionet.software
Subject: Markov Process Software
Date: 21 Jul 92 16:20:52 GMT
Distribution: usa
Organization: University of Washington, Seattle

I am looking for a program (preferentially Mac) to do Markov process
simulations. Any help would be appreciated.

Please reply to
ech5w@u.washington.edu

Thanks,

Chris Homan
From: ness@aecom.yu.edu (Seth Ness)
Newsgroups: bionet.software
Subject: gcg
Date: 23 Jul 92 20:00:15 GMT
Distribution: bionet

hi,
we have GCG on a vax/vms system here. is there any way to print from GCG
(or the vax) to a non-networked printer? in my case i use ncsa telnet on
my mac and would like to print on my private laserwriter thats connected
to the mac by localtalk(i'm connected to the vax by ethernet)

-- 
 Seth L. Ness                        Ness Gadol Hayah Sham          
 Ness@aecom.yu.edu                                                  
Newsgroups: bionet.software
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: Re: XQS?
Organization: EMBnet Switzerland [Basel]
Distribution: bionet
Date: Fri, 31 Jul 1992 17:37:44 GMT


In article <1992Jul31.143605.18041@gserv1.dl.ac.uk>, ray@uk.ac.le ("Dr R. Dalgleish") writes:
|> Has anybody any information about the database query program XQS? I believe
|> that it is a UNIX replacement for the PSQ package from NBRF. Can anybody help
|> with more info?
|> 
|> Thanks,
|> 
|> Raymond Dalgleish.

XQS was the successor for PSQ/NAQ by providing the ability to address multiple
databases simultaneously. Still, the current XQS version is VMS bound. 

XQS is copyrightes software from NBRF/ PIR International.

I forwarded your question to PIR international in Munich, so you might 
get an update on the current software products available for UNIX, VMS, PCs
etc. 


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: BIONET@EARN.FRCGM51
Newsgroups: bionet.software
Subject: Hemagglutinin structures
Date: 23 Jul 92 11:45:00 GMT
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: IN%"bio-software@daresbury.ac.uk"


 
        In response to Y. Pouliot's inquiry: as far as I can see, there are
three hemagglutinin structures from influenza virus:
 
1) mutant Gly116 --> Asp in chain ha1
2) mutant Leu226 --> Gln in chain ha1
3) mutant Asp112 --> Gly in chain ha2
 
        Hope it helps ....
 
---
J-L. Risler                                     Bionet@frcgm51.bitnet
Centre de Genetique Moleculaire                 Risler@frcgm51.bitnet
91190 Gif sur Yvette   France
From: pf@bilbo.bio.purdue.edu (Paul Furbacher)
Newsgroups: bionet.software
Subject: MACAW updated beyond ver 1.0?
Date: 23 Jul 92 05:22:49 GMT
Distribution: bionet.software
Organization: Purdue University

Has the multiple sequence alignment program called MACAW (for 
Windows) been updated from version 1.0?   We like it but it's 
a bit rough as far as on-line help, printing and other features go.

If it has been updated, where is it available?  If not, is there an
expected release date?

Please e-mail to <pf@bilbo.bio.purdue.edu> because we are
not a frequent readers of this group and are likely to miss any
response posted here.  

Thanks.

PF
From: shibumi@turbo.bio.net (Kenton A. Hoover)
Newsgroups: bionet.software
Subject: Re: whatswithblaze?
Date: 24 Jul 92 21:01:49 GMT
Reply-To: shibumi@turbo.bio.net
Organization: GenBank Computing Resource for Mol. Biology

francis@monod.Biol.McGill.CA (Francis Ouellette) writes:
>maybe this is what caused genbank.bio.net to crash ...  ;-)

GenBank crashed due to a drive failure triggered by a power outage on 
Tuesday night.  The drive in question seemed to work after the power failure,
but failed during the night.  The drive was replaced and restored on Wednesday
evening.

| Kenton A. Hoover                                 |                          |
| BIOSCI Network Administrator (bionet newsgroups) |    shibumi@presto.ig.com |
| GenBank/IntelliGenetics, Inc.       415 962 7300 |  shibumi@genbank.bio.net |
|=============================================================================|
|                   Podnimaisa, vstan', mat'rodnaya Rus'!                     |
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.software
Subject: Re:  Molecular Graphics on PCs
Date: 21 Jul 92 19:53:41 GMT
Distribution: bionet

>         Like many others, I'm amazed by the performance/price ratios of the
> i486-based PCs. Three years ago, I was a fan of the Macintosh and
> considered the PCs with some condescencion. Now I'm changing my mind. Even
> the monstruous MS-Windows is quite fast!
>
>         Well, we need here a graphics system to *visualize* protein
> structures. Not edit them and perform huge calculations. Just visualize in
> a comfortable environment. We thought of a SGI Indigo machine. But now...
>
>         Does anyone know a good molecular graphics package for the PC,
> running -for example- under MS-Windows or SCO Unix (X-Windows) ? Can be
> commercial if necessary.
>
>         Thank you.
>
> ---
> J-L. Risler                                     Bionet@frcgm51.bitnet
> Centre de Genetique Moleculaire                 Risler@frcgm51.bitnet
> 91190 Gif sur Yvette   France
>
>
>
>

You might try PCMODEL available as a shareware program.

there are some real possibilities, but software is needed
to convert the Brookhaven to PCMODEL format.  There is a hint
that this program is available on registration ($70.00).
  The main problem with
the Brookhaven format is that PCMODEL requries a connect table.
One would also like the possibility of showing only the alpha
carbon backbone.  This could also be done with the proper manipulation
of the Brookhaven format.  I have tried this on a 486 and
it flies.

there is another commercial program from hyperchem.  This has
been advertised in Science.  It looks very powerful--lets you
do molecular dynamics calculations, etc.  But the price is rather steep.

Jim Cassatt
Newsgroups: bionet.software
From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen)
Subject: re: Macaw and saving color screen output
Organization: University of Western Australia
Date: Wed, 29 Jul 1992 03:44:48 GMT

In article <strom.42@u.washington.edu> strom@u.washington.edu (Mark S. Strom) writes:
>There's been a number of articles posted recently on Macaw, but none seem to 
>touch on the problem described below.
>
>I've recently tried out Macaw 1.05 using Windows 3.1 for sequence alignment 
>of several related proteins.  I really like the color schematic and 
>alignments it gives-in fact, I like it so much I want to make 
>color slides/transparencies of a set for a presentation.  However, this 
>doesn't seem to be easily done.  The only way to export a file (that I can 
>see) is as a text file.  Does anyone know how the screen output could be 
>imported into a graphics program such as Harvard Graphics?  I know there 
>are commercial screen capture programs for Windows that might do this, but 
>I'm a little short of cash right now  8^). 
>
>I have written to Greg Schuler at NCBI for the manual, and maybe this is 
>explained in there, but I thought I'd give this newsgroup a shot too.  
>Thanks to all who may be able to help. 
>
Mark, anything you can show on a screen in Windows 3.1 is capable of
being captured as a bitmap. I haven't got the details here right now,
but I'll follow it up with a post tomorrow. BTW Aldus Persuasion or
MS Powerpoint are great for making color slides for talks !


Robert Coelen
Dept of Microbiology
University of Western Australia
From: news@netnews.upenn.edu (USENET News System)
Newsgroups: bionet.software
Subject: Re: whatswithblaze?
Date: 22 Jul 92 16:07:37 GMT
Followup-To: bionet.software
Organization: University of Pennsylvania

In article <BrspLs.9wB@news.cso.uiuc.edu>,
brett_lindenbach@qms1.life.uiuc.edu (brett lindenbach) wrote:
> 
> The other day I received e-mail from genbank with a release announcement
> of BLAZE 1.0, a MP database similarity searcher. This message instructed
> me to write back for a help file. As of yet, I have not received any reply
> to my requests. Does anyone have this info? 
>      Much obliged,
>              Brett Lindenbach


There was a posting on the bionet.molbio.genbank newsgroup about the queue
software for BLAZE being swamped by all the submissions.

They further urge that you only subnmit one job at a time.

I don't know what they will do about all those searches that were
submitted.
From: eric@bcserv.wustl.edu (Hugo (Eric R.))
Newsgroups: bionet.software
Subject: PDB files and manipulating them on a MSDOS machine
Date: 30 Jul 92 10:56:21 GMT
Organization: Washington University in Saint Louis, MO USA
NNTP-Posting-Host: bcserv.wustl.edu
Summary: Are there any pgms out there for viewing/manipulating PDB files
Keywords: PDB, MSDOS, Windows, 3d animation

Greetings netters,
     My boss (Dr. Carl Frieden) just returned from the Protein
Society meetings in San Diego with an interesting acquisition.
He handed us a CD-ROM disk with the Brookhaven Protein Data Bank
on it. This has prompted us into getting a CD-ROM drive for our
486 machine.  What I would like to know is there any software out
there (public domain, commercial, source code) for viewing and manipulating
these data files on the PC. In the past we've been forced to use SGI
machines in another lab to mess around with PDB files but it would
be very nice if we could do something with them on our PC.  Please
email any suggestions, I will post a summary.   Thanks  ;-{) Eric
-- 
  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
From: JMILLER%BIOVX1.SPAN@STAR.STANFORD.EDU
Newsgroups: bionet.software
Subject: Molecular Graphics on PCs
Date: 22 Jul 92 18:42:03 GMT
Distribution: bionet


  1. Workstations are the only way to go if you want rotatable, high-resolution
color images of biomolecules. However, the prices quoted for having a
workstation vs. a PC are not realistic. Because they are unix machines, you
MUST train someone as a system adminstrator. Either you will have to take some
time learning how to do this (ie., 100's of hours over several months), or
you will have to hire someone to maintain the system. Secondly, you will
HAVE to pay a yearly fee for software upgrades, running in the $1000-$2000
range. Finally, the software ALWAYS costs more than comparable PC software.
The reason that so many people have an Iris and a mac next to each other is
because it is too expensive to buy decent word processors and page layout
programs for the workstations. 
  So the real cost for molecular modeling is: about 15-20k for an iris with
all the trimmings, at least 5k for the modeling software (academic discount),
1-3k yearly for maintaining the system, and whatever it costs to pay you or
someone else to administer the system.
  If all that is needed is visualization, there are Mac and PC based systems
that will display molecules from the coordinates, however slowly and with
limited (8-bit) color. Actual manipulation of structures requires workstation
level software.
-Peter Markiewicz
Xref: sparky bionet.software:1387 comp.binaries.ibm.pc.wanted:5038
From: dcurtis@crc.ac.uk (Dr. David Curtis)
Newsgroups: bionet.software,comp.binaries.ibm.pc.wanted
Subject: Re: REFERENCE managing program needed
Date: 21 Jul 92 10:42:41 GMT
Organization: MRC Human Genome Resource Centre

There is a DOS program for this which I use called REFLIST, early
versions of which are shareware. However I gather the most up to date
version is now only available commercially, though as far as I remember
the registration fee was only in the region of 30$. It does what it says
it does, but the problems I found with it is that it does no store
abstracts and it is rather tedious to enter new data. For these reasons
I actually store all my references in DBase III format using another
Shareware program called PC-File, and then export them to Reflist as
required. I have written little programs that convert from Medline and
one or two other programs into the correct format for PC-File, so that I
can download useful references complete with abstracts from Medline and
then add them to the database where they can be searched for and
browse through. It works for me.

I enclose below a note about Reflist. I imagine it should be findable in
various archives (I got it from one in England). If people are seriously
interested in getting the PC-File header and report files and conversion
programs then let me know and I will see about making them available.


Dave Curtis

Academic Department of Psychiatry,    Janet:       dcurtis@UK.AC.CRC
St. Mary's Hospital,                  Elsewhere:   dcurtis@CRC.AC.UK
Praed Street, London W2.              EARN/Bitnet: dcurtis%CRC@UKACRL
Tel 071-725 1993                      Usenet: ...!mcsun!ukc!mrccrc!D.Curtis


        A PROGRAM TO WRITE AND FORMAT REFERENCE LISTS FOR
               SCIENTIFIC AND TECHNICAL MANUSCRIPTS

                     v3.5 - (c) 1984, 1985,1986,1987

                          E.J.Shillitoe
                       5326 Dumfries Drive
                         Houston TX 77096

                          (713) 728-0596




REFLIST is a program for the IBM PC and compatible computers.  It
performs  the  following  tasks  for authors  of  scientific  and
technical manuscripts:


--   REFLIST reads a text file and finds  the  citations to other
     publications.


--   It draws the references out of a Master File and formats the
     reference list according to the style requirements of almost
     any journal.


--   It  can  return to the text file and replace  the  citations
     with the appropriate numbers.


-- 

Dave Curtis

Academic Department of Psychiatry,    Janet:       dcurtis@UK.AC.CRC
Newsgroups: bionet.software
From: tabq7@isuvax.iastate.edu
Subject: Mapmaker
Reply-To: tabq7@isuvax.iastate.edu
Organization: Iowa State University, Ames, Iowa
Date: Thu, 23 Jul 1992 13:15:06 GMT

Anyone know where I can get the MSDOS version of Mapmaker?

Thanks,

Phil
From: jdboer@SOL.UVIC.CA (Johan deBoer)
Newsgroups: bionet.software
Subject: Re: PCMODEL
Date: 21 Jul 92 20:29:49 GMT
Distribution: bionet

I was wondering on which server the PCMODEL program might be available.
I followed the discussion about protein modeling and would sure like to
give it a try.
Can someone tell me where it is?

J.deBoer
Newsgroups: bionet.software
From: hyu@acs.ucalgary.ca (Hongwei Yu)
Subject: Software for enzyme kinetics
Date: Wed, 29 Jul 92 22:08:36 GMT
Distribution: bionet
Organization: The University of Calgary, Alberta
Keywords: enzyme kinetics

I was wondering if anyone know of any enzyme kinetic analysis
software which can be used on a Mac machine.  The parameters that I
would like to analyze are specific activity, s value and Ks, if
possible. Thanks in advance


-- 
Hongwei Yu
Dept of Biological Sciences, Univ of Calgary
**********************************************
Internet Address:   hyu@acs.ucalgary.ca
Xref: sparky bionet.software:1418 bionet.molbio.genbank:434