Extrcting Data From A File!!!!!!!!!!

[setak]

HI ,I am new to this community.I have a problem ,I need to extract a particular set of data from a PDB file.

ATOM 58 N LYS A 4 1.056 -6.780 1.309 1.00 0.00 N
ATOM 80 C LEU A 5 -1.728 -3.541 2.589 1.00 0.00 N
ATOM 99 N VAL A 6 -0.493 -1.237 4.786 1.00 0.00 N
ATOM 115 N ILE A 7 -1.369 1.593 6.323 1.00 0.00 N
ATOM 134 N ASN A 8 -0.003 4.422 7.554 1.00 0.00 N
ATOM 148 CA GLY A 9 -0.870 7.244 8.066 1.00 0.00 N
ATOM 155 N LYS A 10 -1.156 10.860 8.465 1.00 0.00 N
ATOM 177 N THR A 11 -3.682 11.632 9.106 1.00 0.00 N
ATOM 191 CA LEU A 12 -5.325 9.585 8.210 1.00 0.00 N


this is a example of a my file.At first I needed to extract the lines which have CA at the 3rd position.I used this script(windows XP)
code:

#!usr/bin/perl -w
open(FILE,"<2OED.pdb") or die "cant open file:$!\n";
open(FILE1,">a.txt") or die "cant open file:$!\n";
@pro=<FILE>;
@atom=grep{$_=~/^ATOM\s+/}@pro;
@atoms1=grep{$_=~/^ATOM\s+\d+\s+CA\s+/}@atom;
print FILE1"@atoms1";
close FILE;
close FILE1;
 

This is working finely.But now I need to extract the underlined portion or digits from the file and print them to another.(note:=the digits are not originally underlined,I used that only for indicating)

plz help.

[numberwhun]

HI ,I am new to this community.I have a problem ,I need to extract a particular set of data from a PDB file.

ATOM 58 N LYS A 4 1.056 -6.780 1.309 1.00 0.00 N
ATOM 80 C LEU A 5 -1.728 -3.541 2.589 1.00 0.00 N
ATOM 99 N VAL A 6 -0.493 -1.237 4.786 1.00 0.00 N
ATOM 115 N ILE A 7 -1.369 1.593 6.323 1.00 0.00 N
ATOM 134 N ASN A 8 -0.003 4.422 7.554 1.00 0.00 N
ATOM 148 CA GLY A 9 -0.870 7.244 8.066 1.00 0.00 N
ATOM 155 N LYS A 10 -1.156 10.860 8.465 1.00 0.00 N
ATOM 177 N THR A 11 -3.682 11.632 9.106 1.00 0.00 N
ATOM 191 CA LEU A 12 -5.325 9.585 8.210 1.00 0.00 N


this is a example of a my file.At first I needed to extract the lines which have CA at the 3rd position.I used this script(windows XP)
code:

#!usr/bin/perl -w
open(FILE,"<2OED.pdb") or die "cant open file:$!\n";
open(FILE1,">a.txt") or die "cant open file:$!\n";
@pro=<FILE>;
@atom=grep{$_=~/^ATOM\s+/}@pro;
@atoms1=grep{$_=~/^ATOM\s+\d+\s+CA\s+/}@atom;
print FILE1"@atoms1";
close FILE;
close FILE1;
 

This is working finely.But now I need to extract the underlined portion or digits from the file and print them to another.(note:=the digits are not originally underlined,I used that only for indicating)

plz help.

First off, before I get to your question, I understand that you are new to the forum, but that does not stop you from reading the sticky message at the top of the forum. If you had read it, you would have seen that code tags are required. I have added them for you this time, but please be sure and use them next time.

As for your data, I would use the split() function to split each line of data and grab the elements that you want.

Regards,

Jeff