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NAME:     DIBUG - Biosym Users Group.

   Description:  The DIBUG ("Discover, Insight, Biosym Users' Group")
      list, an unmoderated mailing list for discussion of Biosym products,
      is maintained by Biosym software users and researchers. Expected
      topics of discussion include, but are not limited to, queries about how
      to use features of the software, and how to solve scientific problems
      using the software.  Although this list is administered by and for
      Biosym users, it is expected that the vendor monitors the list, and
      perhaps to respond to issues that may arise. The list is archived and
      archives are accessible via gopher and ftp.
   Subjects:    General aspects of molecular modeling, molecular dynamics,
      ab-initio and semiempirical methods, meeting announcements, nmr
      and xray crystallography data evaluation, aspects of force field usage
      and application, efficiency of use.
   Editor:   Witek Rudnicki, ICM, University of Warsaw, Banacha 2, 
      02-097 Warsaw. POLAND, PH: +48-(2)-658-4306 FX +48-(2)-6584307
   Comments:     Unmoderated.  No subscription restrictions.  50 mes-
      sages/month.  450 subscribers.  Archived.  List type: UNIX. Ad-
      ministrative address:    Distribution  address:
   Archives: WWW:

  1.  Welcome to DIBUG!
  3.  How to access DIBUG archives


                           Welcome to DIBUG!

[[ You will receive this notice either upon subscribing or upon requesting 
a change of email address.  Sending this message is, for me, a good way of 
checking that mail gets through -- or at least does not bounce. ]]

Welcome to DIBUG ("Discovery, Insight, Biosym Users' Group"), an unmoderated 
mailing list for discussion of Biosym products.  Expected topics of discussion 
include, but are not limited to, queries about how to use features of the 
software, and how to solve scientific problems using the software.  Although 
this list is administered by and for Biosym users, we expect Biosym 
Technologies, Inc. to monitor the list, and perhaps to respond to issues that 
may arise.

Mail sent to:

will be immediately resent to all current DIBUG subscribers.  When responding
to a query posted to the list, please reply to the list, unless there is a
reason you prefer to limit your response to the poster, only.  To reply to
the list, rather than the poster, you may have to do something special,
since the poster's path appears on the "From:" line, and the dibug path
appears on the "To:" line.

To request to be added or deleted from the subscriber list, send electronic 
mail to:          

The return path will usually be taken from the From: line of your electronic 
mail, unless you specify an alternative path.  Right now, list maintenance
is being done manually, so there is no set format for specifying things;
just use English.

To send mail directly to the administrator of the list, send mail to              

The administrator is currently 
|    Dr. Reinhard Doelz            | RFC         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142051::embnet     |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 2078    | 
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- is the SWISS EMBnet node ----------------+

All mail sent to DIBUG will be archived at bioftp (see below). 


                         REPORTING BIOSYM BUGS

Gene Plagge of the Biosym Response Center was kind enough to supply the
following information on reporting bugs to Biosym.  You will note that
a bug report to this forum (ie, the DIBUG mailing list) will be heeded.  
I would like to prepend a few unofficial remarks as written by the 
previous list administrator P.Shenkin: 

" Learning a product as complex as Insight/Discover/Etc. is a long undertaking,
and sometimes it's hard to know what is a bug and what is just confusion
due to the fact that one does not yet know all the ins and outs of the 
software.  In my opinion, DIBUG can serve as a forum for either sort of
problem.  Often an informal request to the list stating briefly what you 
are trying to do and what problem you are having will elicit one or more 
responses from the user community saying, in effect, "I've been there, and 
the way to go is this."

Sometimes, however, one becomes convinced that there really is a bug, and if
so, the civic-minded thing to do is to report it formally.  In this case,
you have the responsibility to be as explicit as you possibly can.  The
best way to do this is to try to come up with the minimum set of explicit
procedures which demonstrates the buggy behavior.  This takes effort, but it
generally clarifies the exact nature of the problem both to you and to the 
poor guy at Biosym who's going to have to try to duplicate it and fix it.  
The more explicit you are, and the shorter you can make this bug-demonstrating 
procedure, the greater the chance that it will be fixed sooner, rather than 
later.  In fact, if you are sufficiently clear and concise, other users who 
see your posting to the list will probably try your procedure out, and might 
be able to help you.  Please do not forget to tell what hardware, version of
the OS and version of the Biosym software you are using.

In any case, if you do receive help or figure out on your own how to solve
the problem, please summarize to the list what worked, for the benefit both 
of other subscribers and of the Biosym Response Center, who may be 
simultaneously struggling with your problem.
" (End quote )

Gene's response follows:
> Peter (and all others out there),
> Yes, Biosym is listening to this forum....
> For any future bugs, you can use one of many avenues to report them to
> Biosym:
> 1. This forum.
> 2. Email to us at:
> 3. FAX a report of the bug to the Response Center at 619-458-0431
> 4. Phone in a report to the Response Center at 619-546-5509
> Please include in your report the following information:
> Biosym Product and release number
> Hardware Manufacturer and model number
> Special Hardware (like stereo)
> Operating system and release number
> Detailed description of the bug, with the specific steps you took, so
>   that we can reproduce the bug here.
> When we receive the bug report, we will reproduce it here, and
> enter it into the bug tracking data base. In the event it's not a bug,
> we will let you know how to proceed.
> Thanks for your support of BIOSYM's products!
> Gene Plagge
> BIOSYM Response Center
> 10065 Barnes Canyon Rd.
> San Diego, CA  92121


                       How to access DIBUG archives.

1) anonymous fto to (, changing to

230 Guest login ok, access restrictions apply.
Remote system type is UNIX.
ftp> cd DIBUG-mailinglist
ftp> ls
total 1118
-rw-r--r--   1 boss     manager      120 Apr 20 19:33 .hostdata
-rwxrwxrwx   2 2911     embnet      8474 Apr 19 20:54 current
-rw-r--r--   1 2911     manager   131332 Apr 20 09:29 dibug-18apr92
-rw-r--r--   1 2911     manager   214476 Apr 20 09:29 dibug-21feb92
-rw-r--r--   1 2911     manager   216757 Apr 20 09:30 dibug-6jul91

2) via gopher. GOPHER is a very interesting browsing tool which enables 
you to read in archives, do database searches, and more. The gopher server
at bioftp has been established a few months ago, and is now making 
the dibug archives available as well. I reindex the archive each day. 
If you have questions or comments on the GOPHER software, you can get 
in contact with the Gopher development team by sending e-mail to:


If you are interested in news about new gopher servers and software
you can subscribe to the gopher-news mailing list by sending e-mail

If you want to get the most recent releases of the gopher software, 
you can get these via anonymous ftp from in
the /pub/gopher directory.

I keep a binary depository for gopher executables preconfigured for 
accessing bioftp in the directory programs/gopher-binaries: 

   3 -r-xr-xr-x   1 boss     manager     1248 Mar 13 11:33 README
 368 -rw-r--r--   1 boss     manager   188416 Mar 13 11:25 gopher.Convex
 541 -rwxr-xr-x   1 boss     manager   276708 Mar 13 11:25 gopher.IRIX4.0
 256 -rw-r--r--   1 boss     manager   131072 Mar 13 11:22 gopher.SUN
 202 -rw-r--r--   1 boss     manager   103424 Mar 13 11:14 gopher.ULTRIX-32
 320 -rw-r--r--   1 boss     manager   163840 Mar 13 11:23 gopher.ULTRIX4.1

All you need is to binary ftp the correct image, and then 
% setenv TERM vt100 
% gopher 

                    Internet Gopher Information Client v0.7

                                 Root Directory

          1.  About Gopher, and this bioftp site/
   -->    2.  DIBUG [Discover Insight Biosym User Group] Mailing list/
          3.  EMBnet Services/
          4.  Molecular Biology Archive List.
          5.  and if you have suggestions or problems....
          6.  bioftp server: READ ME FIRST.
          7.  bioftp server: data on EMBL CD-ROM/
          8.  bioftp server: small databases/
          9.  more GOPHERs (biological and others)/

You select option 2 by typing 2   and get 

                    Internet Gopher Information Client v0.7

            DIBUG [Discover Insight Biosym User Group] Mailing list

   -->    1.  Search the mailing list archives for a keyword  
          2.  current/
          3.  dibug-18apr92/
          4.  dibug-21feb92/
          5.  dibug-6jul91/

If you hit  again you can search for a keyword. E.g., searching 
indigo, gives us 
                    Internet Gopher Information Client v0.7

            Search the mailing list archives for a keyword : indigo

   -->    1.  gene@iris4 Re: Re:  Indigo support by Biosym?.
          2.  shenkin (P Re: Indigo support by Biosym?.
          3.  CAMBPRMS@u Re: Re:  Indigo support by Biosym?.
          4.  Reinhard D Re: Last call for new list admin in the US.

and the first hit would be the mail from Gene Plagge... 
Modified: Thu Feb 11 21:38:22 1999 GMT
Page accessed 6575 times since Sat Apr 17 21:21:02 1999 GMT