Thanks Roger,

that worked perfectly!

I'll try and have fun with aline now.

ciao,

s

On May 25, 2010, at 7:56 PM, Roger Dodd wrote:

Hi there,

I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken:

1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz (the newer -503 version didn't work)
2. Change into the directory
3. Execute perl Makefile.PL
4. make
5. make test
6. sudo make install

Hopefully that should get things working.

Cheers,

Roger

On 25 May 2010 17:50, Sebastiano Pasqualato <[log in to unmask]> wrote:

Hi there,
I remember a friend of mine showing me Aline, and it looked very nice.
However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3).
With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages.
That's how I added the path info:

export ALINEHOME='/sw64/share/xtal/aline_011208'
export PATH=$PATH:$ALINEHOME/bin

however, I still get an error while trying to run aline:

Seba@host005:~> aline
Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37.
BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37.
Seba@host005:~>

I even tried with the

perl -MCPAN -e 'install Tk'

command, as suggested by the website, but nothing changed.

Any idea of what's wrong here?
Thanks a lot for the tips,
ciao
s

On May 25, 2010, at 5:47 AM, Charlie Bond wrote:

> Hi Victor,
> Thanks for recommending ALINE.
>
> It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained!
>
> Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality.
>
> Cheers,
> Charlie
>
> Victor Alves wrote:
>> Hi Mohd
>> You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures)
>> http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
>> It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped  :-(
>> Cheers
>> Victor Alves
>>   *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf Of *Salameh, Mohd A., Ph.D.
>> *Sent:* sexta-feira, 21 de Maio de 2010 16:11
>> *To:* [log in to unmask]
>> *Subject:* [ccp4bb] Alignment software
>> Dear All,
>> I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd
>
> --
> Charlie Bond
> Professorial Fellow
> University of Western Australia
> School of Biomedical, Biomolecular and Chemical Sciences
> M310
> 35 Stirling Highway
> Crawley WA 6009
> Australia
> [log in to unmask]
> +61 8 6488 4406

--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 9437 5990

--
Roger B. Dodd, PhD.
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Hills Road
Cambridge
CB2 0XY
UK

-- 

Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094

fax +39 02 9437 5990