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Hi Tom,<br>
<br>
Thanks for updating Sednterp, especially for a version that runs on
Mac.<br>
<br>
I was able to download and run it on my mac but found that there is
a bug. <br>
<br>
So what I am used to do is copy aminoacid sequence from a pdf or
word document and paste into sednterp to calculate vbar and
molecular weight of protein. I was doing the same exercise on the
new version on my mac and discovered that the <b><i>space</i></b>
between aminoacid as well as any space before or after the sequence
is considered as 'CY2' and being added to the animoacid numbers
yielding higher molecular weight and false vbar value.
Interestingly, I found that single space is considered as 2
aminoacids.<br>
<br>
I tried reporting this bug on your wiki but there is no way I was
able to do so as John mentioned in his e-mail.<br>
<br>
Also, retrieving database information takes long time on mac.<br>
<br>
Thanks again,<br>
<br>
Trushar
<pre class="moz-signature" cols="72">===================================
Trushar R. Patel
Postdoctoral Fellow,
Department of Chemistry, 144-Dysart Road,
University of Manitoba, Winnipeg,
Manitoba, R3T2N2- Canada
+ 1 (0) 204-4747172 (O)
<a class="moz-txt-link-abbreviated" href="mailto:patelt@cc.umanitoba.ca">patelt@cc.umanitoba.ca</a> or <a class="moz-txt-link-abbreviated" href="mailto:trushar7@hotmail.com">trushar7@hotmail.com</a>
skype: trushar7
<a class="moz-txt-link-freetext" href="http://home.cc.umanitoba.ca/~patelt">http://home.cc.umanitoba.ca/~patelt</a>
Think green, save Environment
===================================</pre>
<br>
On 12-02-02 2:33 PM, John Philo wrote:
<blockquote cite="mid:6538DC1F332C44D48C3C94E8607C6ABA@79B7XD1"
type="cite">
<pre wrap="">Tom, how the hell is one supposed to report bugs on the Wiki? I find a page
for that on the Wiki, but there seems to be no way for me to add anything to
that page, and there are no instructions.
I'm guessing that you have to be logged in to do this, but when you click on
'log in' at the upper right it doesn't even show an entry to create an
account. I tried 'E-mail new password', which does in fact bring up a new
account possibility, but then that fails saying I need administrator
privileges.
Overall I think the program really needs, at a minimum, some installation
documentation, and what it REALLY needs is a true installation program.
There is nothing that even tells a user that they want to bring in the
default database, not just the program files. As I just found out, the
installation fails if you try to unzip the files into some folder other than
the default.
What I was trying to do was have the new version access my current databases
in the version 1.09 folder. But as soon as I tried the File...Open different
experimental database command it locked up (probably because there is no
database in the program folder).
Does this version (the Windows version) in fact have a way to designate the
location of the database to use at startup?
Also FYI I have modified the Download page on my software web site to point
people to the new version and tell them that support is now through BITC.
John
-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:rasmb-bounces@rasmb.bbri.org">rasmb-bounces@rasmb.bbri.org</a> [<a class="moz-txt-link-freetext" href="mailto:rasmb-bounces@rasmb.bbri.org">mailto:rasmb-bounces@rasmb.bbri.org</a>] On
Behalf Of Tom Laue
Sent: Tuesday, December 06, 2011 6:27 AM
To: RASMB
Cc: SueL; Allan Wright, Jr.; Tucker Hurton
Subject: [RASMB] New Sednterp release
Dear all-
The members of the Biomolecular Interaction Technologies Center (BITC) are
pleased to announce the release of the new version of Sednterp. This new
version retains all of the functionality of the original Sednterp, written
by John Philo. Although a complete re-write of the original program, we used
his code as a template (thank you, John). The original Help file, written by
David Hayes, has been converted to a web-based Wiki (thank you, David). A
PDF version of the help file is available for computers that do not have
access to the web. Calculations and logic in the new Sednterp have been
tested against the original version. The new program does not affect the
operation of the old version. Downloads of the installation files may be
obtained from:<a class="moz-txt-link-freetext" href="http://bitcwiki.sr.unh.edu">http://bitcwiki.sr.unh.edu</a>
There are several significant new features in Sednterp:
1- Desktop Sednterp versions are available for PC, Mac (32 and 64 bit OS),
and Linux. A web-based version will be available in January 2012. A public
version of this will be served from the BITC web site at UNH. This site will
allow data and new functions to be shared (more below). Private versions of
this web-based version also will be available for use behind firewalls. An
announcement will be made when it is available.
2- An "Import database" function is available that will allow you to
incorporate any of your existing Sednterp data into the new version.
3- Perhaps the biggest addition to Sednterp is that it will allow the
seamless addition of new functionality (new tables of data, new user entry
forms, new graphs and reporting) using JavaScript modules. Once a module is
done and tested, it may be downloaded and added by other users to their
programs by copying the module into a special subdirectory. Furthermore, the
same module may be used for the desktop and web-based versions of Sednterp.
Help for the new modules may be added to the Wiki. Two new modules are under
development- one for dn/dc estimates and one for charge calculations. The
development of these modules are being used in the creation of a "Users
Guide" for module development.
Thanks to Tucker Hurton and Allen Wright of the UNH Research Computing
Center for heading up this project, and to the students they have mentored,
Greg Deubler and Bill Bashir, for all of their hard work on this project.
Special thanks are due to the BITC member companies who championed and
funded this work.
Best wishes,
Tom Laue
--
Department of Biochemistry and Molecular Biology University of New Hampshire
Durham, NH 03824-3544
Phone: 603-862-2459
FAX: 603-862-0031
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Tom.Laue@unh.edu">Tom.Laue@unh.edu</a>
<a class="moz-txt-link-abbreviated" href="http://www.bitc.unh.edu">www.bitc.unh.edu</a>
<a class="moz-txt-link-abbreviated" href="http://www.camis.unh.edu">www.camis.unh.edu</a>
_______________________________________________
RASMB mailing list
<a class="moz-txt-link-abbreviated" href="mailto:RASMB@rasmb.bbri.org">RASMB@rasmb.bbri.org</a>
<a class="moz-txt-link-freetext" href="http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb">http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb</a>
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</pre>
</blockquote>
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