[Biopython] Extracting a PDB list

[David Shin]

Hi Patrick,

You should be able to write a script to do this (shell script with some
python or awk).

Off the top of my head, for each file you would:

for each file:
   extract the lines with ^ATOM into a new file to make things easier
   read each line into some list
   subtract the residue number from each line from the next line in the list
      if that value is > 1
          print something ( the file name, or some flag)
      else there are no breaks... can do something else if you want
end

The only tough parts are using spaces to separate items. If say a protein
had 1000 residues, then the 1000 will run into the chain ID. So that's
something to consider. Using specific column numbers would be the better
way.

That and I'm not sure about the uniformity of PDB files that are really old.

Let me know if that helps, if not, I can maybe help out further.

Dave




On Tue, Feb 10, 2015 at 2:24 PM, João Rodrigues <
j.p.g.l.m.rodrigues at gmail.com> wrote:

> Hi,
>
> Without manually checking every single one, there is no such list, at
> least that I know of. Your best bet could be to reduce your resolution as
> low as possible, usually those structures are of very good quality.
>
> Cheers,
>
> João
>
> 2015-02-10 22:35 GMT+01:00 PC <patrick.cossins at inbox.com>:
>
>> Hi,
>>
>> I do know about PISCES lists but I want a list of PDB's without any chain
>> breaks.
>>
>> Is there such a list or a way to obtain such a list?
>>
>> Thank you.
>>
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-- 
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA
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