now I will send the file I need to automatically download....I downloaded it manually, that's the runligplot.pl....because I need to automatically access to the script....to extract information about amminoacidic connections between ligand and receptor...<br>
<br><div class="gmail_quote">2009/4/2 Paola Bisignano <span dir="ltr"><<a href="mailto:paola.bisignano@gmail.com">paola.bisignano@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
thank you....I'm start programming with Perl and it's only a month...I'm very new.... and i couldn't get <br><br><div class="gmail_quote">2009/4/1 marcos rebelo <span dir="ltr"><<a href="mailto:oleber@gmail.com" target="_blank">oleber@gmail.com</a>></span><div>
<div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">2009/4/1 Paola Bisignano <<a href="mailto:paola.bisignano@gmail.com" target="_blank">paola.bisignano@gmail.com</a>>:<br>
<div><div></div><div>><br>
> #!/usr/local/bin/perl<br>
> use LWP::Simple;<br>
> use strict;<br>
> use warnings;<br>
> use LWP 5.64;<br>
> use LWP::UserAgent;<br>
> print "Quale entry di PDB vuoi aprire? ";<br>
> my $pdb=<STDIN>;<br>
> chomp ($pdb);<br>
> my $url1 =<br>
> "<a href="http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb" target="_blank">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb</a>";<br>
> my $content = get $url1;<br>
> die "Couldn't get $url1" unless defined $content;<br>
> while ($content=~ m/uniprot_id=(.*?)&/g)<br>
><br>
> {<br>
> my $code=$1;<br>
> print "ID uniprot: $code\n";<br>
> chomp ($code);<br>
> my $browser =LWP::UserAgent->new;<br>
> my $url = URI-> new ("<a href="http://www.uniprot.org/uniprot/$code.fasta" target="_blank">http://www.uniprot.org/uniprot/$code.fasta</a>");<br>
> my $response=$browser-> get ($url);<br>
> my $fasta=$response->content;<br>
> print "$fasta" ;<br>
> };<br>
><br>
><br>
><br>
><br>
><br>
> this is my script...first I must digit the pdb code (form my test I use<br>
> 1xmj, that I'm sure it has a ligand) I want to explore, (that's the code of<br>
> a protein structure) and then I go to the web page...to extract another<br>
> code, that'uniprot code, so the script thakes that code and put it into<br>
> another web site and estract and print the aminoacidic sequence of the<br>
> protein, then i need to know something about the ligand...and I need to<br>
> access to the file running.pl that brings some information which I have to<br>
> extract....and i don't know what to do<br>
><br>
</div></div><div>> _______________________________________________<br>
> Milan-pm mailing list<br>
> <a href="mailto:Milan-pm@pm.org" target="_blank">Milan-pm@pm.org</a><br>
> <a href="http://mail.pm.org/mailman/listinfo/milan-pm" target="_blank">http://mail.pm.org/mailman/listinfo/milan-pm</a><br>
><br>
><br>
<br>
</div>your code is similar to this simpler code:<br>
<br>
#!/usr/local/bin/perl<br>
use strict;<br>
use warnings;<br>
use LWP::Simple;<br>
<div><br>
print "Quale entry di PDB vuoi aprire? ";<br>
my $pdb = <STDIN>;<br>
chomp ($pdb);<br>
</div>my $url = "<a href="http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb" target="_blank">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb</a>";<br>
my $content = get($url);<br>
die "Couldn't get $url" unless defined $content;<br>
foreach my $code ( $content =~ m/uniprot_id=(.*?)&/g) {<br>
<div> print "ID uniprot: $code\n";<br>
chomp ($code);<br>
</div> my $fasta=get("<a href="http://www.uniprot.org/uniprot/$code.fasta" target="_blank">http://www.uniprot.org/uniprot/$code.fasta</a>");<br>
print "$fasta" ;<br>
};<br>
<br>
<br>
Now, you need to explain your problem to someone that doesn't know<br>
anything about this bio stuff.<br>
<div><div></div><div><br>
Best Regards<br>
Marcos Rebelo<br>
<br>
--<br>
Marcos Rebelo<br>
<a href="http://oleber.freehostia.com" target="_blank">http://oleber.freehostia.com</a><br>
Milan Perl Mongers leader <a href="http://milan.pm.org" target="_blank">http://milan.pm.org</a><br>
_______________________________________________<br>
Milan-pm mailing list<br>
<a href="mailto:Milan-pm@pm.org" target="_blank">Milan-pm@pm.org</a><br>
<a href="http://mail.pm.org/mailman/listinfo/milan-pm" target="_blank">http://mail.pm.org/mailman/listinfo/milan-pm</a><br>
</div></div></blockquote></div></div></div><br>
</blockquote></div><br>