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

Chris Fields cjfields at uiuc.edu
Thu Jan 25 08:37:01 EST 2007


Jian,

Bio::Structure is one area where much work still needs to be done.   
There had been talk on the list a while back about restructuring/ 
refactoring everything there but I have seen little progress as of yet.

Also, it would help tremendously if you attach a simple script to the  
bug report demonstrating the bug for those unfamiliar with  
Bio::Structure (like me!).  This is so we can confirm it and try to  
get a fix in.

cheers!

chris

On Jan 24, 2007, at 6:31 PM, Jian Huang wrote:

> Dear all,
>
> When two or more continuous residues have insertion codes and they  
> are with the same residue name, get_residues() method of  
> Bio::Structure::Entry can only get the first residue. Other residue 
> (s) will be omitted. For example, in PDB structure 1tal, SER-120H  
> will be omitted, although the previous SER-120G will be returned  
> properly. I have reported this bug. See http://bugzilla.open- 
> bio.org/show_bug.cgi?id=2192
>
> It seems that this bug is then actually due to add_residue() method  
> and then and then...Is there any solution to this problem?
>
> Jian Huang
> hjian at kuicr.kyoto-u.ac.jp
>
> Bioinformatics Center,
> Kyoto University
> Gokasho, Uji, Kyoto 611-0011, JAPAN
> Phone: +81-774-38-3296, Fax: +81-774-38-3269
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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