[Biopython] Extracting a PDB list

[David Shin]

Hi Patrick,

I dug up an old PDB parser I wrote for another purpose and made a new
function to find the breaks using the method I suggested, you can maybe
tweak it.

Lenna does bring up some legit concerns. This old script was made to
compare distances, so perhaps you could hack it to try Lenna's Ca-Ca
distance test.

Let me know, and I'll send it to you off list.

Dave


On Tue, Feb 10, 2015 at 6:31 PM, PC <patrick.cossins at inbox.com> wrote:

>  Hi David,
>
> Thank you, yes I am in the process of trying to do this.
>
> Thank you for the suggestion of the spacing too, something I didn't think
> of.
>
> Patrick
>
>
> -----Original Message-----
> *From:* davidsshin at lbl.gov
> *Sent:* Tue, 10 Feb 2015 17:46:35 -0800
> *To:*
> *Subject:* Re: [Biopython] Extracting a PDB list
>
> 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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-- 
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA
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