From jrblesa at ochoa.fib.es  Wed May  5 10:47:37 2004
From: jrblesa at ochoa.fib.es (Jose Rafael Blesa Blesa)
Date: Wed, 5 May 2004 16:47:37 +0200
Subject: [bioknoppix-discuss] (no subject)
Message-ID: <5705200453514473762@ochoa.fib.es>

I'm a new user of BioKnoppix. Maybe my question is very simple,
but... is the version 0.2.1 beta a full working version? When I use
the JEMBOSS tools, the ouput file is always empty. Can someone give
me a hand. Thanks,

Joserra
**********************************************
Jose Rafael Blesa, Ph.D.
Instituto de Investigaciones Citologicas
Amadeo de Saboya, 4
46010 Valencia
Spain

Tel.: +34 963391250
Fax: +34 963601453
E-mail: jrblesa at ochoa.fib.es
**********************************************



From humberto at hpcf.upr.edu  Thu May  6 14:27:11 2004
From: humberto at hpcf.upr.edu (humberto at hpcf.upr.edu)
Date: Thu, 06 May 2004 14:27:11 -0400
Subject: [bioknoppix-discuss] (no subject) 
In-Reply-To: Your message of "Wed, 05 May 2004 16:47:37 +0200."
	<5705200453514473762@ochoa.fib.es> 
Message-ID: <200405061827.i46IRBqt008161@daleth.hpcf.upr.edu>

Jose Rafael Blesa Blesa <jrblesa at ochoa.fib.es> wrote:

> I'm a new user of BioKnoppix. Maybe my question is very simple,
> but... is the version 0.2.1 beta a full working version? 

It should be. I'll admit to not using Jemboss much though.

> When I use the JEMBOSS tools, the ouput file is always empty. Can
> someone give me a hand.

Can you give a more concrete example? I tested out some simple Jemboss
commands, and they mostly work.

For example

showdb
go
Show results

works as I'd expect, as does

showfeat
tembl:xlrhodop
go
Show results

I did notice that if you put anything in the output options or advanced
output options, that the Show results doesn't work. I don't know if
that's a bug or a feature.

I seem to recall having seen at some point graphical programs also work,
but I can't get plotorf to produce anything interesting today.

The command line versions of these tools are working correctly, and
these are the ones we've been using in class. We'll look into the
graphical interfaces for the next release.

-- 
Humberto Ortiz Zuazaga
Programmer-Archaeologist
High Performance Computing facility
University of Puerto Rico
http://www.hpcf.upr.edu/~humberto/
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From humberto at hpcf.upr.edu  Thu May  6 15:47:22 2004
From: humberto at hpcf.upr.edu (humberto at hpcf.upr.edu)
Date: Thu, 06 May 2004 15:47:22 -0400
Subject: [bioknoppix-discuss] (no subject) 
In-Reply-To: Message from humberto@hpcf.upr.edu 
	of "Thu, 06 May 2004 14:27:11 -0400."
	<200405061827.i46IRBqt008161@daleth.hpcf.upr.edu> 
Message-ID: <200405061947.i46JlMsU008505@daleth.hpcf.upr.edu>

Looks like there is a problem with the /usr/local/bin/runJemboss.csh script.

The last line reads:

(cd /usr/local/share/EMBOSS/jemboss; java org/emboss/jemboss/Jemboss local &)

but regular mortals don't have write permissions in the
/usr/local/share/EMOSS/jemboss directory, so it's hard to save your
work.

As a workaround, you can copy the file to your home directory, and edit
it so that the last line reads:

java org/emboss/jemboss/Jemboss local &

and running ./runJemboss.csh from the command line (the menu option
still won't work). Now more stuff works. Graphical output will result in
files like:

plotorf.1.png

being created in your home directory. You can view these with display,
or browse to it in the file manager. We'll fix this in the next release.

-- 
Humberto Ortiz Zuazaga
Programmer-Archaeologist
High Performance Computing facility
University of Puerto Rico
http://www.hpcf.upr.edu/~humberto/
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From aleman at linuxmail.org  Thu May  6 23:12:25 2004
From: aleman at linuxmail.org (Stephan Aleman)
Date: Thu, 06 May 2004 19:12:25 -0800
Subject: [bioknoppix-discuss] (no subject)
Message-ID: <20040507031225.C2AE723ABE@ws5-3.us4.outblaze.com>

I recently downloaded BioKnoppix and tried JEMBOSS in KDE.

My Open Source Users Group is interested in demonstrating 3d protein structure folding in high resolution, are any of these graphical applications included in BioKnoppix 0.2.1?

Stephan Aleman
Vice President
fosug.org
~/~


----- Original Message -----
From: humberto at hpcf.upr.edu
Date: Thu, 06 May 2004 14:27:11 -0400
To: "Jose Rafael Blesa Blesa" <jrblesa at ochoa.fib.es>
Subject: Re: [bioknoppix-discuss] (no subject) 

> Jose Rafael Blesa Blesa <jrblesa at ochoa.fib.es> wrote:
> 
> > I'm a new user of BioKnoppix. Maybe my question is very simple,
> > but... is the version 0.2.1 beta a full working version? 
> 
> It should be. I'll admit to not using Jemboss much though.
> 
> > When I use the JEMBOSS tools, the ouput file is always empty. Can
> > someone give me a hand.
> 
> Can you give a more concrete example? I tested out some simple Jemboss
> commands, and they mostly work.
> 
> For example
> 
> showdb
> go
> Show results
> 
> works as I'd expect, as does
> 
> showfeat
> tembl:xlrhodop
> go
> Show results
> 
> I did notice that if you put anything in the output options or advanced
> output options, that the Show results doesn't work. I don't know if
> that's a bug or a feature.
> 
> I seem to recall having seen at some point graphical programs also work,
> but I can't get plotorf to produce anything interesting today.
> 
> The command line versions of these tools are working correctly, and
> these are the ones we've been using in class. We'll look into the
> graphical interfaces for the next release.
> 
> -- 
> Humberto Ortiz Zuazaga
> Programmer-Archaeologist
> High Performance Computing facility
> University of Puerto Rico
> http://www.hpcf.upr.edu/~humberto/

>
> _______________________________________________
> bioknoppix-discuss mailing list
> bioknoppix-discuss at lists.hpcf.upr.edu
> http://lists.hpcf.upr.edu/mailman/listinfo/bioknoppix-discuss

-- 
______________________________________________
Check out the latest SMS services @ http://www.linuxmail.org 
This allows you to send and receive SMS through your mailbox.


Powered by Outblaze


From humberto at hpcf.upr.edu  Mon May 10 11:50:28 2004
From: humberto at hpcf.upr.edu (Humberto Ortiz Zuazaga)
Date: Mon, 10 May 2004 11:50:28 -0400
Subject: Protein structure viewers (was Re: [bioknoppix-discuss] (no subject))
In-Reply-To: Your message of "Thu, 06 May 2004 19:12:25 PST."
	<20040507031225.C2AE723ABE@ws5-3.us4.outblaze.com> 
Message-ID: <200405101550.i4AFoStl027451@daleth.hpcf.upr.edu>

Stephan Aleman <aleman at linuxmail.org> wrote:

> I recently downloaded BioKnoppix and tried JEMBOSS in KDE.
> 
> My Open Source Users Group is interested in demonstrating 3d protein
> structure folding in high resolution, are any of these graphical
> applications included in BioKnoppix 0.2.1?

The 0.2.1 release has rasmol and Cn3D, both described on the applications page:

http://bioknoppix.hpcf.upr.edu/applications

There are some nicer protein structure viewers, but the ones we have
seen have restrictions on redistribution, preventing us from including
them on the bioknoppix disk.

rasmol and Cn3D work for .pdb files and the structure databases at NCBI.

-- 
Humberto Ortiz Zuazaga
Programmer-Archaeologist
High Performance Computing facility
University of Puerto Rico
http://www.hpcf.upr.edu/~humberto/
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From deejoe at raccoon.com  Mon May 10 12:02:31 2004
From: deejoe at raccoon.com (D. Joe Anderson)
Date: Mon, 10 May 2004 11:02:31 -0500
Subject: Protein structure viewers (was Re: [bioknoppix-discuss] (no
	subject))
In-Reply-To: <200405101550.i4AFoStl027451@daleth.hpcf.upr.edu>
References: <20040507031225.C2AE723ABE@ws5-3.us4.outblaze.com>
	<200405101550.i4AFoStl027451@daleth.hpcf.upr.edu>
Message-ID: <20040510160231.GA26983@raccoon.com>

On Mon, May 10, 2004 at 11:50:28AM -0400, Humberto Ortiz Zuazaga wrote:

> The 0.2.1 release has rasmol and Cn3D, both described on the applications page:
> 
> http://bioknoppix.hpcf.upr.edu/applications
> 
> There are some nicer protein structure viewers, but the ones we have
> seen have restrictions on redistribution, preventing us from including
> them on the bioknoppix disk.
> 
> rasmol and Cn3D work for .pdb files and the structure databases at NCBI.

PyMOL is a free software protein structure viewer.  

As a plus for bioknoppix, it is being actively maintained for Debian
by Michael Banck, and so should be easily apt-get'table into a future
version of bioknoppix.  

--Joe




From aleman at linuxmail.org  Mon May 10 23:00:58 2004
From: aleman at linuxmail.org (Stephan Aleman)
Date: Mon, 10 May 2004 19:00:58 -0800
Subject: Protein structure viewers (was Re: [bioknoppix-discuss]
	(nosubject))
Message-ID: <20040511030058.8C9643983FB@ws5-1.us4.outblaze.com>

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