Morten,
I was made aware of this thread (see below) thanks to a colleague.
Your juvenile self-indulgence and paranoia amuses me. While it was
indeed a genuine oversight that caused your credit -- it was I who
included your credit in first place, if I remember correctly -- to be
deleted from the manual page, I will now *make it a point* to *remove*
your man page from every future distribution of MUSTANG--- and there is
a major one coming very soon!
Since you have chosen to make a mountain out of a molehill, are you
really squabbling for credit for merely formatting in troff the text
which the program *itself* generates? There was not a *single word* of
your own in that man page. The entire thing was taken /in toto/ from the
paper's abstract, the programs "--help" option and the original README
file. In fact, I was really thankful even for this (and included your
name in the man page) and would still have, had it not been for your
repugnant attitude!. What is /really/ "troublesome" for a scientist is
to piggyback on someone else's software and seek credit for some
inconsequential trivia; and then shout out from rooftops for a genuine
oversight!
You say that you sent me a mail making me aware of this. First, it has
been over a year and a half since I left Penn State, and more than four
years since I left c...@unimelb. Nevertheless I keep checking these
inboxes periodically. It was, then, very surprising that I missed your
mail. So I vigorously searched these accounts (including the junk
folders; and no mail ever gets deleted). Turns out that I still can't
trace your mail??? Can you prove that you really sent a mail to me? The
way you conduct yourself (and this is not the first time I have seen you
casting aspersions) makes me suspect everything you say!
I care two hoots about the package's future status in Debian-Med. I have
more than just deep admiration for the philosophy of free software and
have always been a strong advocate of open-source software myself. It
would be a shame if Debian is sabotaged by sheer unreason!
Arun Konagurthu
I am in the akward position that an upstream author has removed the
attribution in the Authors section in a man page that I have contributed.
See the attached diff.
I wrote an email making him aware of this, but have not received any reply.
I think this is especially troublesome for someone aspiring to become a
scientist.
The man page was originally covered by the license in debian/copyright,
which said:
Copyright: of the Debian packaging is assigned to the copyright holder and
condition to the above license.
License: BSD-like
However, I don't think that gives permission to remove the author's name.
What do you think?
Cheers,
Morten
-- Morten Kjeldgaard, asc. professor, MSc, PhD BiRC - Bioinformatics
Research Center, Aarhus University C. F. Møllers Alle, Building 1110,
DK-8000 Aarhus C, Denmark. Lab +45 8942 3130 * Fax +45 8942 3077 *
Home +45 8618 8180 Mobile +45 5186 0147 * http://www.bioxray.au.dk/~mok
------------------------------------------------------------------------
--- MUSTANG_v.3/mustang 2008-01-15 02:05:19.000000000 +0100
+++ MUSTANG_v3.2/man/mustang.1 2009-04-18 10:44:53.000000000 +0200
@@ -62,9 +62,9 @@
options the user specifies in the command line.
DEFAULT output identifier: 'results'
.TP
-.BI \-F " <fmt>"
-Alignment output format. The choices for \fI<fmt>\fR are: 'html', 'fasta',
- 'pir', 'msf'. DEFAULT format: 'html'
+.BI \-F " <format>"
+Alignment output format. The choices for \fI<format>\fR are: 'html', 'fasta',
+\'pir\', 'msf'. DEFAULT format: 'html'
.TP
.BI \-D " [CA\-CA diameter]"
Produce an HTML file where the the residues are reported in lower case with
@@ -75,6 +75,10 @@
Generate a PDB file containing optimal superposition of all the structures
based on the alignment. DEFAULT: 'ON'.
.TP
+.BI \-r " [<ON>/<OFF>]"
+Print to a file rmsd table of multiple superposition along with rotation matrix
+and translation vector corresponding to each input structure. DEFAULT: 'OFF'.
+.TP
.B \-\-help
display a help message and exits.
.TP
@@ -83,13 +87,14 @@
.SH AUTHORS
\fBMustang\fR was written by A. S. Konagurthu, using the algorithm of
-A. S. Konagurthu \fIet al.\fR (see reference)
-.PP
-This manual page was written by Morten Kjeldgaard <m...@bioxray.dk>.
+A. S. Konagurthu \fIet al.\fR (see REFERENCE)
.SH REFERENCE
A. S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk, MUSTANG: A
multiple structural alignment algorithm, \fBProteins, 64(3) 559-574 (2006).\fR
+.SH BUG REPORT
+arun AT csse DOT unimelb DOT edu DOT au
+
.SH SEE ALSO
-\fBMustang\fR's homepage: http://www.cs.mu.oz.au/~arun/mustang/
+\fBMustang\fR's homepage: http://www.csse.unimelb.edu.au/~arun/mustang/
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