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 > <sebastiano.pasqual...@ifom-ieo-campus.it> 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: > > s...@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. > s...@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:ccp...@jiscmail.ac.uk] *On Behalf Of > >> *Salameh, Mohd A., Ph.D. > >> *Sent:* sexta-feira, 21 de Maio de 2010 16:11 > >> *To:* CCP4BB@JISCMAIL.AC.UK > >> *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 > > charles.b...@uwa.edu.au > > +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
