From aengus.stewart at cancer.org.uk  Fri Jan 14 12:36:52 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 14 Jan 2005 17:36:52 +0000
Subject: [EMBOSS] Jemboss - nondisplay of files in File Manager
Message-ID: <41E80334.7080708@cancer.org.uk>


Hi,

I have just solved an unusual problem that a user had.

He could see his files on the server at the command line but not through the Jemboss File Manager.  If he created a new file through Jemboss it appeared in the File Manager until refresh was hit - where upon it disappeared!

I have worked out he had a number of files that started with the control char - \033 which is Escape and when Jemboss got hold of it cleared the File Manager display.

Dont know if other CTRL chars have same effect though............



Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From pmr at ebi.ac.uk  Thu Jan 20 11:50:39 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 20 Jan 2005 16:50:39 +0000
Subject: [EMBOSS] Re: [EMBOSS-BUG] bizarre behaviour of remap
In-Reply-To: <20050120164600.GA26824@bigben.ulb.ac.be>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
Message-ID: <41EFE15F.6050105@ebi.ac.uk>

Guy Bottu wrote:

> 	Dear friends,
> 
> I just noticed the following. I am running EMBOSS 2.9.0 under CompaqTru64 
> 5.1B. When I run  :
> remap -orfminsize=300 embl:af049064
> I get a file with bizarre characters where you would expect spaces and -
> (see attachment)
> Yet I installed EMBOSS 2.9.0 mid August 2004 and I did not see this 
> before. Is it a behaviour of EMBOSS or is there an interference with 
> something else in our system ? Did anyone ever observe similar behaviour ?

We had one report of this problem earlier. It is fixed in the next release.

The cause is a cut site which goes past the start/end of the sequence.

The fix involved restructuring the pattern matching code to hold more 
information, and there are too many dependencies, I think, to build a 
patchfile from the current code.

For this and some other recent fixes we may make a new release quite soon.

Hope this helps,

Peter



From sbassi at gmail.com  Thu Jan 20 12:33:18 2005
From: sbassi at gmail.com (Sebastian Bassi)
Date: Thu, 20 Jan 2005 09:33:18 -0800
Subject: [EMBOSS] Re: [EMBOSS-BUG] bizarre behaviour of remap
In-Reply-To: <41EFE15F.6050105@ebi.ac.uk>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
	 <41EFE15F.6050105@ebi.ac.uk>
Message-ID: <b43bf208050120093336b68d2e@mail.gmail.com>

On Thu, 20 Jan 2005 16:50:39 +0000, Peter Rice <pmr at ebi.ac.uk> wrote:
> For this and some other recent fixes we may make a new release quite soon.

Regarding a new release, please remember about the posibility to
change default colors in Abiview. I have to modify the source code now
to change the default colors.
Thank you very much!


-- 
<a href="http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1">La
web sin popups ni spyware: Usa Firefox en lugar de Internet
Explorer</a>


From Peter.Robinson at t-online.de  Thu Jan 20 15:37:54 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Thu, 20 Jan 2005 21:37:54 +0100
Subject: [EMBOSS] psiphi
In-Reply-To: <b43bf208050120093336b68d2e@mail.gmail.com>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
	 <41EFE15F.6050105@ebi.ac.uk>  <b43bf208050120093336b68d2e@mail.gmail.com>
Message-ID: <1106253474.3336.19.camel@localhost.localdomain>

Hi EMBOSSers,

I have used the wonderful programm psiphi to learn how to calculate
these angles and have borrowed parts of the code for a larger program
that does some datamining in PDB files. This program will be a smallish
part of a mainly biological paper we are hoping to submit soon, and I
was wondering about how to best quote this program, given that it does
not seem to be on the list of applications on the WWW server (I got it
from the EMBOSS CD that was distributed at the Bioinformatics meeting in
Glasgow last Summer).

-Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From aengus.stewart at cancer.org.uk  Fri Jan 21 08:42:22 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 21 Jan 2005 13:42:22 +0000
Subject: [EMBOSS] emboss.default
Message-ID: <41F106BE.70402@cancer.org.uk>


I just want to double check something.

Can I use more than one file name ie Can I do this?

file: est_rod*.dat est_mus*.dat

in specifying a data library?


Also are there any plans to roll entret and seqret into one - surely it would be quite easy to get seqret to return all of the entry rather than just the top 8 doc lines? perhaps -doclines=8 could maintain this functionality.  Its just I have found it hard to explain to users that there are 2 programs that do every so slightly different things..........


Oh and any news about the new indexing?


Sorry for all the questions but I am knee deep in EMBOSS based stuff at the moment.


Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From pmr at ebi.ac.uk  Fri Jan 21 08:57:09 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 21 Jan 2005 13:57:09 +0000
Subject: [EMBOSS] emboss.default
In-Reply-To: <41F106BE.70402@cancer.org.uk>
References: <41F106BE.70402@cancer.org.uk>
Message-ID: <41F10A35.8020700@ebi.ac.uk>

Aengus Stewart wrote:

> I just want to double check something. 
> Can I use more than one file name ie Can I do this? 
> file: est_rod*.dat est_mus*.dat
> in specifying a data library?

Yes. Tested and known to work in 2.9.0 - probably worked in earlier releases, 
but not for all variations.

You can also include everything and use a list for the exclude value.

> Also are there any plans to roll entret and seqret into one 

Tricky. Entret specifically reports the original text. seqret parses it, uses 
it, and reports what it can in the output format.

Yes, seqret shoould parse out and retain more information (no doubt you have 
noticed that the -feat option does retain the feature table). I will take a 
look at how much of EMBL, GenBank and SwissProt formats can be preserved.

But we will still need entret.

> Oh and any news about the new indexing?

To be included as a beta version in the next release.

> Sorry for all the questions but I am knee deep in EMBOSS based stuff at 
> the moment.

Knee deep? I hope that was a compliment :-)

Peter



From ableasby at hgmp.mrc.ac.uk  Fri Jan 21 09:40:11 2005
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Fri, 21 Jan 2005 14:40:11 GMT
Subject: [EMBOSS] emboss.default
Message-ID: <200501211440.j0LEeBCc011523@bromine.hgmp.mrc.ac.uk>

>> Oh and any news about the new indexing?
>To be included as a beta version in the next release.

Best not to take that as being definitive. The good news
is that the KW/DE/OS/OC was finished yesterday. The bad
news is that it hasn't been tested yet. The ID/AC/SV code
has been ready for some time but not incorporated.

Delays have been rather unavoidable and unpredictable given
the funding circumstances; they may well continue in that
fashion until matters are resolved.

The next EMBOSS release (2.10.0) may happen soon. That release
will sort out issues to do with alignments, Jemboss (Java 1.5)
etc. The indexing code cannot be incorporated in that
timescale.

Alan


From gbottu at ben.vub.ac.be  Fri Jan 21 10:11:25 2005
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 21 Jan 2005 16:11:25 +0100
Subject: [EMBOSS] emboss.default
In-Reply-To: <41F10A35.8020700@ebi.ac.uk>
References: <41F106BE.70402@cancer.org.uk> <41F10A35.8020700@ebi.ac.uk>
Message-ID: <20050121151125.GA3286@bigben.ulb.ac.be>

On Fri, Jan 21, 2005 at 01:57:09PM +0000, Peter Rice wrote:
> Aengus Stewart wrote:
> >Also are there any plans to roll entret and seqret into one 
> 
> Tricky. Entret specifically reports the original text. seqret parses it, 
> uses it, and reports what it can in the output format.
> 
> Yes, seqret shoould parse out and retain more information (no doubt you 
> have noticed that the -feat option does retain the feature table). I will 
> take a look at how much of EMBL, GenBank and SwissProt formats can be 
> preserved.

maybe the occasion to use the new library functions to modify textsearch 
so that it can, if requested by the user, search in the complete 
documentation (or a part of it), rather then just in the DE line, 
reproducing the functionality of GCG stringsearch (mode B) ?

	Guy Bottu,
	Belgian EMBnet Node



From kkmattil at csc.fi  Mon Jan 24 08:59:56 2005
From: kkmattil at csc.fi (Kimmo Mattila)
Date: Mon, 24 Jan 2005 15:59:56 +0200 (EET)
Subject: [EMBOSS] EMBOSS interface for InsightII
Message-ID: <Pine.LNX.4.61.0501241543560.32541@sampo.csc.fi>


Hi,

I have written a set of scripts to create a simple EMBOSS interface to 
insightII molecular modeling program. InsightII is a commercial 
molecular modeling program by Acclerys so it is not freely available.
However, if you have InsightII and EMBOSS installed to your 
machine and you wish to test the EMBOSS interface, please feel free to 
download the scripts from URL:

http://www.csc.fi/chem/progs/insightII_csc.phtml.en#EMBOSS

The insight_EMBOSS.tar file, which you can download from the URL above, 
contains a README that describes the installation process. In the best 
case all you need to do is to set up your insightII environment and run 
an installation script.

When the scripts are installed, an EMBOSS menu will appear to your 
Homology module menu list. Note that you can apply EMBOSS commands only 
to those sequences that have been read in into the sequence window of 
insightII. The only exception to this is seqret, which you can use to 
read sequences to the sequence window. The results can be used to create 
plots, color residue regions or to define atom subsets.

The InsightII EMBOSS interface is focused to those EMBOSS tools, that do 
not have a counterpart in InsightII. The homology modeling module of 
insightII includes for example sequence alignment tools and thus programs 
like needle or water are not included. At the moment interface scripts are 
available for following EMBOSS programs:

   antigenic
   charge
   digest
   dotmatcher
   fuzzpro
   helixturnhelix
   hmoment
   iep
   infoalign
   octanol
   patmatmotifs
   pepinfo
   pepnet
   pepstats
   pepwheel
   plotcon
   polydot
   prettyplot
   seqret
   sigcleave
   tmap

Any comments and suggestions about the interface are welcome but please 
remember that the scripts are not produced by any official programming 
project. They are just a kind of side product of a research project.

Regards,

Kimmo Mattila



---------------------------------------------------------------
Kimmo Mattila, sovellusasiantuntija, Bioinformatiikan palvelut, CSC
PL 405 02101 Espoo, puh 09 457 2708 , fax (09) 457 2302
CSC on tieteen tietotekniikan keskus, www.csc.fi, s-posti: 
kimmo.mattila at csc.fi

Kimmo Mattila, application scientist, Bioinformatics Support, CSC
P.O. Box 405 02101 Espoo, Finland, tel +358 9 4572708, fax +358 9 4572302
CSC is the Finnish IT Center for Science, www.csc.fi, e-mail: 
kimmo.mattila at csc.fi
---------------------------------------------------------------


From stephen.taylor at molecular-sciences.oxford.ac.uk  Tue Jan 25 03:40:48 2005
From: stephen.taylor at molecular-sciences.oxford.ac.uk (Steve Taylor)
Date: Tue, 25 Jan 2005 08:40:48 -0000
Subject: [EMBOSS] JEMBOSS 
In-Reply-To: <41F10A35.8020700@ebi.ac.uk>
Message-ID: <E1CtMFm-00015e-3n@smtp2.herald.ox.ac.uk>

Hi,

I am using the following configuration:

EMBOSS 2.9.0, Solaris 9, JEMBOSS 1.3 Standalone.

When I try and use seqret within JEMBOSS to fetch 'genbankrelease:ab000111' ( I have also tried with other db:accession
combinations)

Error:execvp['getz -e '[genbankrelease-id:ab000111]|[genbankrelease-acc:ab000111]",NULL)failed:'No such file or directory'
Error:Unable to read sequence 'genbankrelease:ab000111'
Died:seqret terminated:Bad value for '-sequence' with -auto defined

seqret with this accession works fine on the standard EMBOSS command line. Is there some extra configuration that needs doing?

Many thanks for any help,

Steve
--------------------------------------------
Computational Biology Research Group
Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Tel: +44 (0)1865 (2)85732 (Dunn)
Tel: +44 (0)1865 (2)22640 (WIMM)
Web: http://www.compbio.ox.ac.uk








From Peter.Robinson at t-online.de  Wed Jan 26 15:53:40 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Wed, 26 Jan 2005 21:53:40 +0100
Subject: [EMBOSS] ramachandran
Message-ID: <1106772819.3230.20.camel@localhost.localdomain>

Dear EMBOSS list,

I would like to be able to create a Ramachandran plot from a list of
hundreds or thousands of pairs of psi,phi angles and display this
together with the defined allowed areas. Although this is all pretty
straightforward, I have not been able to find an open source tool with
which to do this and am thinking about reinventing this wheel. So I
wonder:

1) Does anyone know of an open source ramachandran plotter?
2) If not, is there an EMBOSS graphics program which might lend itself
to be adapted to this? I know something about programming nongraphical
applications in EMBOSS thanks to the course given by Alan and Jon and
subsequent experiments, but not too much about the graphical
capabilities. I was thinking of using code as described here
alpha2.bmc.uu.se/gerard/rama/ramarev.html 
to define the ramachandran core areas and then a simple graphics routine
to plot the psi/phi pairs from my own datamining expedition as simple
points onto the plot.

Thanks,

Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From Peter.Robinson at t-online.de  Wed Jan 26 17:46:53 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Wed, 26 Jan 2005 23:46:53 +0100
Subject: [EMBOSS] DOMAINATRIX
Message-ID: <1106779613.30365.4.camel@localhost.localdomain>

Dear list,

another question:

I would like to install the DOMAINATRIX applications. After doing the
usual 
./configure
make

I get the errors
make[1]: *** No rule to make target `../../../nucleus/libnucleus.la',
needed by `contacts'.  Stop.

I am not sure I understand what is going on, since I though the nucleus
directory was only a part of the main EMBOSS source tree. Can anybody
give me a quick tip on this? I have EMBOSS 2.9 installed and working on
my system (Debian linux sarge, 2.6 kernel, EMBOSS install "normally",
i.e. without apt-get).

THanks, Peter


-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From David.Bauer at SCHERING.DE  Thu Jan 27 01:32:13 2005
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Thu, 27 Jan 2005 07:32:13 +0100
Subject: Antwort: [EMBOSS] DOMAINATRIX
Message-ID: <OF4EE2B361.0F0D1ACC-ONC1256F96.00238174-C1256F96.0023E8B5@schering.de>


Hi Peter,

where did you untar the DOMAINATRIX-1.0.0.tar.gz ?
Because this is an embassy package it must reside in a subdirectory named
"embassy" under the main EMBOSS source tree.
So if the EMBOSS sources are in ......./EMBOSS-2.9.0
it must be in EMBOSS-2.9.0/embassy/DOMAINATRIX-1.0.0

Hope this helps,
David.



                                                                                                                           
                      Peter.Robinson at t                                                                                     
                      -online.de                                                                                           
                      (Peter Robinson)         An:      emboss at hgmp.mrc.ac.uk                                              
                      Gesendet von:            Kopie:                                                                      
                      owner-emboss at hgm         Thema:   [EMBOSS] DOMAINATRIX                                               
                      p.mrc.ac.uk                                                                                          
                                                                                                                           
                                                                                                                           
                      26.01.2005 23:46                                                                                     
                                                                                                                           
                                                                                                                           




Dear list,

another question:

I would like to install the DOMAINATRIX applications. After doing the
usual
./configure
make

I get the errors
make[1]: *** No rule to make target `../../../nucleus/libnucleus.la',
needed by `contacts'.  Stop.

I am not sure I understand what is going on, since I though the nucleus
directory was only a part of the main EMBOSS source tree. Can anybody
give me a quick tip on this? I have EMBOSS 2.9 installed and working on
my system (Debian linux sarge, 2.6 kernel, EMBOSS install "normally",
i.e. without apt-get).

THanks, Peter


--
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/








From deejoe at iastate.edu  Thu Jan 27 11:29:36 2005
From: deejoe at iastate.edu (D. Joe Anderson)
Date: Thu, 27 Jan 2005 10:29:36 -0600
Subject: [EMBOSS] ramachandran
In-Reply-To: <20050127162440.GA25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain> <20050127162440.GA25697@iastate.edu>
Message-ID: <20050127162936.GB25697@iastate.edu>

On Thu, Jan 27, 2005 at 10:24:40AM -0600, D. Joe Anderson wrote:
> On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:
> 
> > 1) Does anyone know of an open source ramachandran plotter?
> 
> garlic is GPL'd, and has the ability to make Ramachandran plots,
> so maybe there's some code there that would be suitable.

Sorry, forgot to include links:

  Garlic Home Page
  http://garlic.mefos.hr/garlic-1.0/

The distribution of Garlic I've looked at (only to confirm that
it makes Ramachandran plots, I'm not [yet] a heavy user of it:

  Debian -- Debian Package Search Results                
  http://packages.debian.org/cgi-bin/search_packages.pl?searchon=names&version=all&exact=1&keywords=garlic

-- 
D. Joe Anderson, Asst. Sci.            2252 Molecular Biology Bldg.     
BBMB Research Computing Support
www.bb.iastate.edu/computing           bbsupport at iastate.edu 


From deejoe at iastate.edu  Thu Jan 27 11:24:40 2005
From: deejoe at iastate.edu (D. Joe Anderson)
Date: Thu, 27 Jan 2005 10:24:40 -0600
Subject: [EMBOSS] ramachandran
In-Reply-To: <1106772819.3230.20.camel@localhost.localdomain>
References: <1106772819.3230.20.camel@localhost.localdomain>
Message-ID: <20050127162440.GA25697@iastate.edu>

On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:

> 1) Does anyone know of an open source ramachandran plotter?

garlic is GPL'd, and has the ability to make Ramachandran plots,
so maybe there's some code there that would be suitable.

-- 
D. Joe Anderson, Asst. Sci.            2252 Molecular Biology Bldg.     
BBMB Research Computing Support
www.bb.iastate.edu/computing           bbsupport at iastate.edu 


From Peter.Robinson at t-online.de  Thu Jan 27 15:17:33 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Thu, 27 Jan 2005 21:17:33 +0100
Subject: [EMBOSS] ramachandran
In-Reply-To: <20050127162936.GB25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain>
	 <20050127162440.GA25697@iastate.edu>  <20050127162936.GB25697@iastate.edu>
Message-ID: <1106857053.3238.5.camel@localhost.localdomain>

On Thu, 2005-01-27 at 17:29, D. Joe Anderson wrote:
> On Thu, Jan 27, 2005 at 10:24:40AM -0600, D. Joe Anderson wrote:
> > On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:
> > 
> > > 1) Does anyone know of an open source ramachandran plotter?
> > 
> > garlic is GPL'd, and has the ability to make Ramachandran plots,
> > so maybe there's some code there that would be suitable.
> 
> Sorry, forgot to include links:
> 
>   Garlic Home Page
>   http://garlic.mefos.hr/garlic-1.0/
> 
> The distribution of Garlic I've looked at (only to confirm that
> it makes Ramachandran plots, I'm not [yet] a heavy user of it:
> 
>   Debian -- Debian Package Search Results                
>   http://packages.debian.org/cgi-bin/search_packages.pl?searchon=names&version=all&exact=1&keywords=garlic

Thanks for the tip. It's nice that there's a Debian package. I will take
a look into the source code once I figure out the program and see if it
is adapatable to what I need.
-peter

-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From aengus.stewart at cancer.org.uk  Fri Jan 28 14:26:12 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 28 Jan 2005 19:26:12 +0000
Subject: [EMBOSS] codon usage tables
Message-ID: <41FA91D4.8080703@cancer.org.uk>


Hi,

Anyone have a list to decypher the filenames in /data/CODONS.

I wanted to be able to explain the filenames to users.

I can quite easily build new files from CUTG - is this a better thing to do?


Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From scott at cs.wits.ac.za  Mon Jan 31 14:19:59 2005
From: scott at cs.wits.ac.za (Scott Hazelhurst)
Date: Mon, 31 Jan 2005 21:19:59 +0200 (SAST)
Subject: [EMBOSS] Jemboss server -- Client won't start
Message-ID: <20050131191959.5F1F613E7A8@midi.cs.wits.ac.za>



I am trying to set up Jemboss in client-server mode and have been
struggling.

The current situation is that I think I have set everything up
properly (run error messages anyway).

If I run the runJemboss script on the server machine, everything seems
to be OK.

If I try to run a web client, I get the  following behaviour
-- JWS starts, downloads all the jars, checks certificates,  and seems
   happy
-- it asks whether I want to start the application, when I say "Start"
   I get a window that appears, saying "Starting application...." 
   which then doesn't change (at least > 15 mins).

The big problem is that this is all fail-silent so I have no idea of
where in the chain the problem is. Can anyone suggest of places where
I can look to see what the problem is? Any obvious log files  etc.

Many thanks for any help,

Scott

-- 





From Peter.Robinson at t-online.de  Mon Jan 31 15:04:26 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Mon, 31 Jan 2005 21:04:26 +0100
Subject: [EMBOSS] pdbparse format
In-Reply-To: <20050127162440.GA25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain>
	 <20050127162440.GA25697@iastate.edu>
Message-ID: <1107201866.3241.21.camel@localhost.localdomain>

Hi list,

I have been looking into the new pdbparse program and am writing a
routine to parse the output of that program into a Java program I am
writing to do some datamining on PDB files. For the moment at least I am
writing a parse routine based on column positions rather than on regular
expressions or some other approach.
I would appreciate some help in understanding the output format. I have
been looking at the function ajPdbWriteAll. 

ajFmtPrintF(outf, "%-2c%6S    %-4S%8.3f%9.3f%9.3f<snip>, 
				    tmp->Id1, 
				    tmp->Id3,
				    tmp->Atm, 
				    tmp->X, 
				    tmp->Y, 
				    tmp->Z,
				    <snip>
				    

this should print out the 
"%-2c":  1char AA (left-justified, 2 spaces)
"%6S    ": 3charAA (right-justified, 6 spaces, followed by 4 spaces)
"-4S": AtomType (e.g., CA) (left-justified, 4 spaces)
"%8.3" x coord, 8 spaces with 3 precision 
"%9.3" y coord  9 spaces with 3 precision
"%9.3" z coord  9 spaces with 3 precision

==> If I am reading this correctly, why does the x coord have one less
space than y and z?
==> Can one consider this output format fixed, or will it be subject to
changes?
==> Excuse what may seem like a trivial question, but I don't want my
program to break down "at an embarassing moment". 

Thanks,
Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/




From aengus.stewart at cancer.org.uk  Fri Jan 14 17:36:52 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 14 Jan 2005 17:36:52 +0000
Subject: [EMBOSS] Jemboss - nondisplay of files in File Manager
Message-ID: <41E80334.7080708@cancer.org.uk>


Hi,

I have just solved an unusual problem that a user had.

He could see his files on the server at the command line but not through the Jemboss File Manager.  If he created a new file through Jemboss it appeared in the File Manager until refresh was hit - where upon it disappeared!

I have worked out he had a number of files that started with the control char - \033 which is Escape and when Jemboss got hold of it cleared the File Manager display.

Dont know if other CTRL chars have same effect though............



Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From pmr at ebi.ac.uk  Thu Jan 20 16:50:39 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 20 Jan 2005 16:50:39 +0000
Subject: [EMBOSS] Re: [EMBOSS-BUG] bizarre behaviour of remap
In-Reply-To: <20050120164600.GA26824@bigben.ulb.ac.be>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
Message-ID: <41EFE15F.6050105@ebi.ac.uk>

Guy Bottu wrote:

> 	Dear friends,
> 
> I just noticed the following. I am running EMBOSS 2.9.0 under CompaqTru64 
> 5.1B. When I run  :
> remap -orfminsize=300 embl:af049064
> I get a file with bizarre characters where you would expect spaces and -
> (see attachment)
> Yet I installed EMBOSS 2.9.0 mid August 2004 and I did not see this 
> before. Is it a behaviour of EMBOSS or is there an interference with 
> something else in our system ? Did anyone ever observe similar behaviour ?

We had one report of this problem earlier. It is fixed in the next release.

The cause is a cut site which goes past the start/end of the sequence.

The fix involved restructuring the pattern matching code to hold more 
information, and there are too many dependencies, I think, to build a 
patchfile from the current code.

For this and some other recent fixes we may make a new release quite soon.

Hope this helps,

Peter



From sbassi at gmail.com  Thu Jan 20 17:33:18 2005
From: sbassi at gmail.com (Sebastian Bassi)
Date: Thu, 20 Jan 2005 09:33:18 -0800
Subject: [EMBOSS] Re: [EMBOSS-BUG] bizarre behaviour of remap
In-Reply-To: <41EFE15F.6050105@ebi.ac.uk>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
	 <41EFE15F.6050105@ebi.ac.uk>
Message-ID: <b43bf208050120093336b68d2e@mail.gmail.com>

On Thu, 20 Jan 2005 16:50:39 +0000, Peter Rice <pmr at ebi.ac.uk> wrote:
> For this and some other recent fixes we may make a new release quite soon.

Regarding a new release, please remember about the posibility to
change default colors in Abiview. I have to modify the source code now
to change the default colors.
Thank you very much!


-- 
<a href="http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1">La
web sin popups ni spyware: Usa Firefox en lugar de Internet
Explorer</a>


From Peter.Robinson at t-online.de  Thu Jan 20 20:37:54 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Thu, 20 Jan 2005 21:37:54 +0100
Subject: [EMBOSS] psiphi
In-Reply-To: <b43bf208050120093336b68d2e@mail.gmail.com>
References: <20050120164600.GA26824@bigben.ulb.ac.be>
	 <41EFE15F.6050105@ebi.ac.uk>  <b43bf208050120093336b68d2e@mail.gmail.com>
Message-ID: <1106253474.3336.19.camel@localhost.localdomain>

Hi EMBOSSers,

I have used the wonderful programm psiphi to learn how to calculate
these angles and have borrowed parts of the code for a larger program
that does some datamining in PDB files. This program will be a smallish
part of a mainly biological paper we are hoping to submit soon, and I
was wondering about how to best quote this program, given that it does
not seem to be on the list of applications on the WWW server (I got it
from the EMBOSS CD that was distributed at the Bioinformatics meeting in
Glasgow last Summer).

-Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From aengus.stewart at cancer.org.uk  Fri Jan 21 13:42:22 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 21 Jan 2005 13:42:22 +0000
Subject: [EMBOSS] emboss.default
Message-ID: <41F106BE.70402@cancer.org.uk>


I just want to double check something.

Can I use more than one file name ie Can I do this?

file: est_rod*.dat est_mus*.dat

in specifying a data library?


Also are there any plans to roll entret and seqret into one - surely it would be quite easy to get seqret to return all of the entry rather than just the top 8 doc lines? perhaps -doclines=8 could maintain this functionality.  Its just I have found it hard to explain to users that there are 2 programs that do every so slightly different things..........


Oh and any news about the new indexing?


Sorry for all the questions but I am knee deep in EMBOSS based stuff at the moment.


Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From pmr at ebi.ac.uk  Fri Jan 21 13:57:09 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 21 Jan 2005 13:57:09 +0000
Subject: [EMBOSS] emboss.default
In-Reply-To: <41F106BE.70402@cancer.org.uk>
References: <41F106BE.70402@cancer.org.uk>
Message-ID: <41F10A35.8020700@ebi.ac.uk>

Aengus Stewart wrote:

> I just want to double check something. 
> Can I use more than one file name ie Can I do this? 
> file: est_rod*.dat est_mus*.dat
> in specifying a data library?

Yes. Tested and known to work in 2.9.0 - probably worked in earlier releases, 
but not for all variations.

You can also include everything and use a list for the exclude value.

> Also are there any plans to roll entret and seqret into one 

Tricky. Entret specifically reports the original text. seqret parses it, uses 
it, and reports what it can in the output format.

Yes, seqret shoould parse out and retain more information (no doubt you have 
noticed that the -feat option does retain the feature table). I will take a 
look at how much of EMBL, GenBank and SwissProt formats can be preserved.

But we will still need entret.

> Oh and any news about the new indexing?

To be included as a beta version in the next release.

> Sorry for all the questions but I am knee deep in EMBOSS based stuff at 
> the moment.

Knee deep? I hope that was a compliment :-)

Peter



From ableasby at hgmp.mrc.ac.uk  Fri Jan 21 14:40:11 2005
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Fri, 21 Jan 2005 14:40:11 GMT
Subject: [EMBOSS] emboss.default
Message-ID: <200501211440.j0LEeBCc011523@bromine.hgmp.mrc.ac.uk>

>> Oh and any news about the new indexing?
>To be included as a beta version in the next release.

Best not to take that as being definitive. The good news
is that the KW/DE/OS/OC was finished yesterday. The bad
news is that it hasn't been tested yet. The ID/AC/SV code
has been ready for some time but not incorporated.

Delays have been rather unavoidable and unpredictable given
the funding circumstances; they may well continue in that
fashion until matters are resolved.

The next EMBOSS release (2.10.0) may happen soon. That release
will sort out issues to do with alignments, Jemboss (Java 1.5)
etc. The indexing code cannot be incorporated in that
timescale.

Alan


From gbottu at ben.vub.ac.be  Fri Jan 21 15:11:25 2005
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 21 Jan 2005 16:11:25 +0100
Subject: [EMBOSS] emboss.default
In-Reply-To: <41F10A35.8020700@ebi.ac.uk>
References: <41F106BE.70402@cancer.org.uk> <41F10A35.8020700@ebi.ac.uk>
Message-ID: <20050121151125.GA3286@bigben.ulb.ac.be>

On Fri, Jan 21, 2005 at 01:57:09PM +0000, Peter Rice wrote:
> Aengus Stewart wrote:
> >Also are there any plans to roll entret and seqret into one 
> 
> Tricky. Entret specifically reports the original text. seqret parses it, 
> uses it, and reports what it can in the output format.
> 
> Yes, seqret shoould parse out and retain more information (no doubt you 
> have noticed that the -feat option does retain the feature table). I will 
> take a look at how much of EMBL, GenBank and SwissProt formats can be 
> preserved.

maybe the occasion to use the new library functions to modify textsearch 
so that it can, if requested by the user, search in the complete 
documentation (or a part of it), rather then just in the DE line, 
reproducing the functionality of GCG stringsearch (mode B) ?

	Guy Bottu,
	Belgian EMBnet Node



From kkmattil at csc.fi  Mon Jan 24 13:59:56 2005
From: kkmattil at csc.fi (Kimmo Mattila)
Date: Mon, 24 Jan 2005 15:59:56 +0200 (EET)
Subject: [EMBOSS] EMBOSS interface for InsightII
Message-ID: <Pine.LNX.4.61.0501241543560.32541@sampo.csc.fi>


Hi,

I have written a set of scripts to create a simple EMBOSS interface to 
insightII molecular modeling program. InsightII is a commercial 
molecular modeling program by Acclerys so it is not freely available.
However, if you have InsightII and EMBOSS installed to your 
machine and you wish to test the EMBOSS interface, please feel free to 
download the scripts from URL:

http://www.csc.fi/chem/progs/insightII_csc.phtml.en#EMBOSS

The insight_EMBOSS.tar file, which you can download from the URL above, 
contains a README that describes the installation process. In the best 
case all you need to do is to set up your insightII environment and run 
an installation script.

When the scripts are installed, an EMBOSS menu will appear to your 
Homology module menu list. Note that you can apply EMBOSS commands only 
to those sequences that have been read in into the sequence window of 
insightII. The only exception to this is seqret, which you can use to 
read sequences to the sequence window. The results can be used to create 
plots, color residue regions or to define atom subsets.

The InsightII EMBOSS interface is focused to those EMBOSS tools, that do 
not have a counterpart in InsightII. The homology modeling module of 
insightII includes for example sequence alignment tools and thus programs 
like needle or water are not included. At the moment interface scripts are 
available for following EMBOSS programs:

   antigenic
   charge
   digest
   dotmatcher
   fuzzpro
   helixturnhelix
   hmoment
   iep
   infoalign
   octanol
   patmatmotifs
   pepinfo
   pepnet
   pepstats
   pepwheel
   plotcon
   polydot
   prettyplot
   seqret
   sigcleave
   tmap

Any comments and suggestions about the interface are welcome but please 
remember that the scripts are not produced by any official programming 
project. They are just a kind of side product of a research project.

Regards,

Kimmo Mattila



---------------------------------------------------------------
Kimmo Mattila, sovellusasiantuntija, Bioinformatiikan palvelut, CSC
PL 405 02101 Espoo, puh 09 457 2708 , fax (09) 457 2302
CSC on tieteen tietotekniikan keskus, www.csc.fi, s-posti: 
kimmo.mattila at csc.fi

Kimmo Mattila, application scientist, Bioinformatics Support, CSC
P.O. Box 405 02101 Espoo, Finland, tel +358 9 4572708, fax +358 9 4572302
CSC is the Finnish IT Center for Science, www.csc.fi, e-mail: 
kimmo.mattila at csc.fi
---------------------------------------------------------------


From stephen.taylor at molecular-sciences.oxford.ac.uk  Tue Jan 25 08:40:48 2005
From: stephen.taylor at molecular-sciences.oxford.ac.uk (Steve Taylor)
Date: Tue, 25 Jan 2005 08:40:48 -0000
Subject: [EMBOSS] JEMBOSS 
In-Reply-To: <41F10A35.8020700@ebi.ac.uk>
Message-ID: <E1CtMFm-00015e-3n@smtp2.herald.ox.ac.uk>

Hi,

I am using the following configuration:

EMBOSS 2.9.0, Solaris 9, JEMBOSS 1.3 Standalone.

When I try and use seqret within JEMBOSS to fetch 'genbankrelease:ab000111' ( I have also tried with other db:accession
combinations)

Error:execvp['getz -e '[genbankrelease-id:ab000111]|[genbankrelease-acc:ab000111]",NULL)failed:'No such file or directory'
Error:Unable to read sequence 'genbankrelease:ab000111'
Died:seqret terminated:Bad value for '-sequence' with -auto defined

seqret with this accession works fine on the standard EMBOSS command line. Is there some extra configuration that needs doing?

Many thanks for any help,

Steve
--------------------------------------------
Computational Biology Research Group
Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Tel: +44 (0)1865 (2)85732 (Dunn)
Tel: +44 (0)1865 (2)22640 (WIMM)
Web: http://www.compbio.ox.ac.uk








From Peter.Robinson at t-online.de  Wed Jan 26 20:53:40 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Wed, 26 Jan 2005 21:53:40 +0100
Subject: [EMBOSS] ramachandran
Message-ID: <1106772819.3230.20.camel@localhost.localdomain>

Dear EMBOSS list,

I would like to be able to create a Ramachandran plot from a list of
hundreds or thousands of pairs of psi,phi angles and display this
together with the defined allowed areas. Although this is all pretty
straightforward, I have not been able to find an open source tool with
which to do this and am thinking about reinventing this wheel. So I
wonder:

1) Does anyone know of an open source ramachandran plotter?
2) If not, is there an EMBOSS graphics program which might lend itself
to be adapted to this? I know something about programming nongraphical
applications in EMBOSS thanks to the course given by Alan and Jon and
subsequent experiments, but not too much about the graphical
capabilities. I was thinking of using code as described here
alpha2.bmc.uu.se/gerard/rama/ramarev.html 
to define the ramachandran core areas and then a simple graphics routine
to plot the psi/phi pairs from my own datamining expedition as simple
points onto the plot.

Thanks,

Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From Peter.Robinson at t-online.de  Wed Jan 26 22:46:53 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Wed, 26 Jan 2005 23:46:53 +0100
Subject: [EMBOSS] DOMAINATRIX
Message-ID: <1106779613.30365.4.camel@localhost.localdomain>

Dear list,

another question:

I would like to install the DOMAINATRIX applications. After doing the
usual 
./configure
make

I get the errors
make[1]: *** No rule to make target `../../../nucleus/libnucleus.la',
needed by `contacts'.  Stop.

I am not sure I understand what is going on, since I though the nucleus
directory was only a part of the main EMBOSS source tree. Can anybody
give me a quick tip on this? I have EMBOSS 2.9 installed and working on
my system (Debian linux sarge, 2.6 kernel, EMBOSS install "normally",
i.e. without apt-get).

THanks, Peter


-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From David.Bauer at SCHERING.DE  Thu Jan 27 06:32:13 2005
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Thu, 27 Jan 2005 07:32:13 +0100
Subject: Antwort: [EMBOSS] DOMAINATRIX
Message-ID: <OF4EE2B361.0F0D1ACC-ONC1256F96.00238174-C1256F96.0023E8B5@schering.de>


Hi Peter,

where did you untar the DOMAINATRIX-1.0.0.tar.gz ?
Because this is an embassy package it must reside in a subdirectory named
"embassy" under the main EMBOSS source tree.
So if the EMBOSS sources are in ......./EMBOSS-2.9.0
it must be in EMBOSS-2.9.0/embassy/DOMAINATRIX-1.0.0

Hope this helps,
David.



                                                                                                                           
                      Peter.Robinson at t                                                                                     
                      -online.de                                                                                           
                      (Peter Robinson)         An:      emboss at hgmp.mrc.ac.uk                                              
                      Gesendet von:            Kopie:                                                                      
                      owner-emboss at hgm         Thema:   [EMBOSS] DOMAINATRIX                                               
                      p.mrc.ac.uk                                                                                          
                                                                                                                           
                                                                                                                           
                      26.01.2005 23:46                                                                                     
                                                                                                                           
                                                                                                                           




Dear list,

another question:

I would like to install the DOMAINATRIX applications. After doing the
usual
./configure
make

I get the errors
make[1]: *** No rule to make target `../../../nucleus/libnucleus.la',
needed by `contacts'.  Stop.

I am not sure I understand what is going on, since I though the nucleus
directory was only a part of the main EMBOSS source tree. Can anybody
give me a quick tip on this? I have EMBOSS 2.9 installed and working on
my system (Debian linux sarge, 2.6 kernel, EMBOSS install "normally",
i.e. without apt-get).

THanks, Peter


--
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/








From deejoe at iastate.edu  Thu Jan 27 16:29:36 2005
From: deejoe at iastate.edu (D. Joe Anderson)
Date: Thu, 27 Jan 2005 10:29:36 -0600
Subject: [EMBOSS] ramachandran
In-Reply-To: <20050127162440.GA25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain> <20050127162440.GA25697@iastate.edu>
Message-ID: <20050127162936.GB25697@iastate.edu>

On Thu, Jan 27, 2005 at 10:24:40AM -0600, D. Joe Anderson wrote:
> On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:
> 
> > 1) Does anyone know of an open source ramachandran plotter?
> 
> garlic is GPL'd, and has the ability to make Ramachandran plots,
> so maybe there's some code there that would be suitable.

Sorry, forgot to include links:

  Garlic Home Page
  http://garlic.mefos.hr/garlic-1.0/

The distribution of Garlic I've looked at (only to confirm that
it makes Ramachandran plots, I'm not [yet] a heavy user of it:

  Debian -- Debian Package Search Results                
  http://packages.debian.org/cgi-bin/search_packages.pl?searchon=names&version=all&exact=1&keywords=garlic

-- 
D. Joe Anderson, Asst. Sci.            2252 Molecular Biology Bldg.     
BBMB Research Computing Support
www.bb.iastate.edu/computing           bbsupport at iastate.edu 


From deejoe at iastate.edu  Thu Jan 27 16:24:40 2005
From: deejoe at iastate.edu (D. Joe Anderson)
Date: Thu, 27 Jan 2005 10:24:40 -0600
Subject: [EMBOSS] ramachandran
In-Reply-To: <1106772819.3230.20.camel@localhost.localdomain>
References: <1106772819.3230.20.camel@localhost.localdomain>
Message-ID: <20050127162440.GA25697@iastate.edu>

On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:

> 1) Does anyone know of an open source ramachandran plotter?

garlic is GPL'd, and has the ability to make Ramachandran plots,
so maybe there's some code there that would be suitable.

-- 
D. Joe Anderson, Asst. Sci.            2252 Molecular Biology Bldg.     
BBMB Research Computing Support
www.bb.iastate.edu/computing           bbsupport at iastate.edu 


From Peter.Robinson at t-online.de  Thu Jan 27 20:17:33 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Thu, 27 Jan 2005 21:17:33 +0100
Subject: [EMBOSS] ramachandran
In-Reply-To: <20050127162936.GB25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain>
	 <20050127162440.GA25697@iastate.edu>  <20050127162936.GB25697@iastate.edu>
Message-ID: <1106857053.3238.5.camel@localhost.localdomain>

On Thu, 2005-01-27 at 17:29, D. Joe Anderson wrote:
> On Thu, Jan 27, 2005 at 10:24:40AM -0600, D. Joe Anderson wrote:
> > On Wed, Jan 26, 2005 at 09:53:40PM +0100, Peter Robinson wrote:
> > 
> > > 1) Does anyone know of an open source ramachandran plotter?
> > 
> > garlic is GPL'd, and has the ability to make Ramachandran plots,
> > so maybe there's some code there that would be suitable.
> 
> Sorry, forgot to include links:
> 
>   Garlic Home Page
>   http://garlic.mefos.hr/garlic-1.0/
> 
> The distribution of Garlic I've looked at (only to confirm that
> it makes Ramachandran plots, I'm not [yet] a heavy user of it:
> 
>   Debian -- Debian Package Search Results                
>   http://packages.debian.org/cgi-bin/search_packages.pl?searchon=names&version=all&exact=1&keywords=garlic

Thanks for the tip. It's nice that there's a Debian package. I will take
a look into the source code once I figure out the program and see if it
is adapatable to what I need.
-peter

-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/



From aengus.stewart at cancer.org.uk  Fri Jan 28 19:26:12 2005
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Fri, 28 Jan 2005 19:26:12 +0000
Subject: [EMBOSS] codon usage tables
Message-ID: <41FA91D4.8080703@cancer.org.uk>


Hi,

Anyone have a list to decypher the filenames in /data/CODONS.

I wanted to be able to explain the filenames to users.

I can quite easily build new files from CUTG - is this a better thing to do?


Aengus

-- 
-----------------------------------------------------------------------
Aengus Stewart
Group Leader
Bioinformatics at CGAL                            Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information  which may be privileged and
confidential.  The information is intended to be for the use of the
individual(s) or entity named above.  If you are not the intended recipient,
be aware that any disclosure, copying, distribution or use of the contents
of this information is prohibited. If you have received this electronic
message in error, please notify me by telephone or email (to the number
or address above) immediately.


From scott at cs.wits.ac.za  Mon Jan 31 19:19:59 2005
From: scott at cs.wits.ac.za (Scott Hazelhurst)
Date: Mon, 31 Jan 2005 21:19:59 +0200 (SAST)
Subject: [EMBOSS] Jemboss server -- Client won't start
Message-ID: <20050131191959.5F1F613E7A8@midi.cs.wits.ac.za>



I am trying to set up Jemboss in client-server mode and have been
struggling.

The current situation is that I think I have set everything up
properly (run error messages anyway).

If I run the runJemboss script on the server machine, everything seems
to be OK.

If I try to run a web client, I get the  following behaviour
-- JWS starts, downloads all the jars, checks certificates,  and seems
   happy
-- it asks whether I want to start the application, when I say "Start"
   I get a window that appears, saying "Starting application...." 
   which then doesn't change (at least > 15 mins).

The big problem is that this is all fail-silent so I have no idea of
where in the chain the problem is. Can anyone suggest of places where
I can look to see what the problem is? Any obvious log files  etc.

Many thanks for any help,

Scott

-- 





From Peter.Robinson at t-online.de  Mon Jan 31 20:04:26 2005
From: Peter.Robinson at t-online.de (Peter Robinson)
Date: Mon, 31 Jan 2005 21:04:26 +0100
Subject: [EMBOSS] pdbparse format
In-Reply-To: <20050127162440.GA25697@iastate.edu>
References: <1106772819.3230.20.camel@localhost.localdomain>
	 <20050127162440.GA25697@iastate.edu>
Message-ID: <1107201866.3241.21.camel@localhost.localdomain>

Hi list,

I have been looking into the new pdbparse program and am writing a
routine to parse the output of that program into a Java program I am
writing to do some datamining on PDB files. For the moment at least I am
writing a parse routine based on column positions rather than on regular
expressions or some other approach.
I would appreciate some help in understanding the output format. I have
been looking at the function ajPdbWriteAll. 

ajFmtPrintF(outf, "%-2c%6S    %-4S%8.3f%9.3f%9.3f<snip>, 
				    tmp->Id1, 
				    tmp->Id3,
				    tmp->Atm, 
				    tmp->X, 
				    tmp->Y, 
				    tmp->Z,
				    <snip>
				    

this should print out the 
"%-2c":  1char AA (left-justified, 2 spaces)
"%6S    ": 3charAA (right-justified, 6 spaces, followed by 4 spaces)
"-4S": AtomType (e.g., CA) (left-justified, 4 spaces)
"%8.3" x coord, 8 spaces with 3 precision 
"%9.3" y coord  9 spaces with 3 precision
"%9.3" z coord  9 spaces with 3 precision

==> If I am reading this correctly, why does the x coord have one less
space than y and z?
==> Can one consider this output format fixed, or will it be subject to
changes?
==> Excuse what may seem like a trivial question, but I don't want my
program to break down "at an embarassing moment". 

Thanks,
Peter



-- 
Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson/