[RASMB] New Sednterp release

Thu Feb 2 13:34:42 PST 2012

Hi Tom,

Thanks for updating Sednterp, especially for a version that runs on Mac.

I was able to download and run it on my mac but found that there is a bug.

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 */space/* 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.

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.

Also, retrieving database information takes long time on mac.

Thanks again,

Trushar

===================================
Trushar R. Patel
Postdoctoral Fellow,
Department of Chemistry, 144-Dysart Road,
University of Manitoba, Winnipeg,
Manitoba, R3T2N2- Canada

+ 1 (0) 204-4747172 (O)
patelt at cc.umanitoba.ca or trushar7 at hotmail.com
skype: trushar7
http://home.cc.umanitoba.ca/~patelt

Think green, save Environment
===================================

On 12-02-02 2:33 PM, John Philo wrote:
> 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: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] 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:http://bitcwiki.sr.unh.edu
>
> 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: Tom.Laue at unh.edu
> www.bitc.unh.edu
> www.camis.unh.edu
>
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