[BioPython] Bio.PDB phi/psi angles

[Peter]

Douglas Kojetin wrote:
> Hi All,
> 
> I would like to print the phi/psi angles for a structure using the  
> script found here:
> 
> http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/ 
> python/ramachandran/calculate/
> 
> but the script chokes on the following line:
> 
> phi_psi = poly.get_phi_psi_list()
> 
> error output:
> 
> Traceback (most recent call last):
>    File "./ramachandran_biopython.py", line 62, in <module>
>      phi_psi = poly.get_phi_psi_list()
>    File "/sw/lib/python2.5/site-packages/Bio/PDB/Polypeptide.py",  
> line 169, in get_phi_psi_list
>      res.xtra["PHI"]=phi
> NameError: global name 'res' is not defined
> 
> Does anyone know what I can do to overcome this problem?

Its not your fault, it looks like an error has crept into
Bio/PDB/Polypeptide.py with revision 1.32 (shipped with biopython 1.43),
which I think I've just fixed with CVS revision 1.33

You can grab the files from here once the webpage has updated:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/PDB/Polypeptide.py?cvsroot=biopython

Just backup and replace the existing file here:
/sw/lib/python2.5/site-packages/Bio/PDB/Polypeptide.py

Or, you could downgrade to biopython 1.42 ;)

Peter