[BioPython] problems to fetch pdb files from server using pdb_list
Florian Koelling
florian.koelling at tu-bs.de
Fri May 23 08:28:40 UTC 2008
Humm - I recognised that I was still using Biopython 1.42 (installed via
synaptics) - it works fine on 1.45! :-))))
Peter wrote:
> On Thu, May 22, 2008 at 3:38 PM, Florian Koelling
> <florian.koelling at tu-bs.de> wrote:
>
>> Hi Folks!
>>
>> I tried to download pdb files using pdb_list:
>> (the second variant didn't work as well:-@)
>>
>> from Bio.PDB import*
>>
>> pdbl=PDBList()
>> pdbl.retrieve_pdb_file('1FAT')
>>
>
> This worked for me, it create a subdirectory "fa" inside the current
> working directory, and saved the PDB there as "pdb1fat.ent".
>
> Are you sure the error you quoted in your email matches this code?
>
>
>> #pdbl.retrieve_pdb_file('1FAT', obsolete= compression='.Z',
>> uncompress='gunzip', pdir='/home/flo/Desktop')
>>
>
> The above isn't valid python syntax (there is something wrong between
> the words obsolete and compression). You probably want something like
> this:
>
> pdbl.retrieve_pdb_file('1FAT', pdir='/home/flo/Desktop')
>
> Peter
>
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