[Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method

[Chris Fields]

On Jan 26, 2007, at 8:52 PM, Jian Huang wrote:

> Dear Chris,
>
> A simple scipt to detect residue leak bug in Bio::Structure::Entry
> get_residues() method...
> You can download a slice of 1TAL structure for test at
> http://bugzilla.open-bio.org/attachment.cgi?id=549
>
> Best regards,
>
> Jian Huang
...

Jian,


I have tested your script out.  I changed the subroutine to return a  
blank string; it was shooting off warnings when they were turned on,,  
but the results were the same w/o any warnings:

Use of uninitialized value in pattern match (m//) at
/Users/cjfields/src/bioperl-live/Bio/Structure/IO/pdb.pm line 449,  
<GEN0> line
105.
LEU-114
LEU-119
PRO-120
ARG-120.AA
VAL-120.BB
ALA-120.CC
ASN-120.DD
GLY-120.EE
SER-120.GG  <----
SER-120.HH  <----
PHE-120.II
VAL-120.JJ
THR-120.KK
VAL-121

Isn't the arrow pointing at SER-120G and SER-120H?

You might want to check that you are running the latest Bioperl  
release (1.5.2); I noticed that a CVS commit that may be related to  
this was made after the 1.5.1 release.  If you have upgraded, an  
older installation may be interfering.  You can check which version  
by running (I think this will work on WinXP):

perl -MBio::Root::Version -e "print $Bio::Root::Version::VERSION,\"\n\""

To locate your bioperl installation being used:

perldoc -l Bio::Root::Root

chris