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
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