Hi Ed, If you are looking for a specific protein, why not get all PDB files
with a DBREF record pointing at the uniprot record of the protein you want? You
can do a simple text search in the PDB, e.g. 'MYG_PHYCA'. Cheers,Robbie
> Date: Fri, 22 Jun 2012 22:39:12 -0400
> From: epozh...@umaryland.edu
> Subject: Re: [ccp4bb] pdb sequence search
> To: CCP4BB@JISCMAIL.AC.UK
>
> Tim,
>
>
> > I did not understand your objection against solution 1 - is it because
> > it is not automated? You can sort the results by max. Ident so that
> > you can sroll down to the limit you set yourself.
>
> More that it does not generate a list of PDB IDs. What I want to do is
> to find every structure of a particular protein and line them all up. I
> am not saying it's not doable with option 1, it's just not too convenient.
> >
> > Why do you think a identity cut-off was a good criterium? I usually
> > cut by E-value because I assume the developers of blast know what they
> > are doing and I have the impression they consider the E-value a better
> > criterium than the max. Ident.
> Because I want all the structures of a particular protein itself, not
> it's homologues. I just went through several cycles of reducing E-value
> down to 1e-100, and I still get one hit included at 88% identity.
> Setting E-value cutoff to 0 doesn't work, it just returns them all.
> Well, thanks to you I now see how to figure out the cutoff - the results
> are sorted by E-values and list them, so I can just go to the first
> non-identical hit and use a slightly smaller number. It's just that
> sequence identity is easier for me to interpret and it's (emotionally)
> easier to select a cutoff at, say, no more than 5 mutations rather than
> E-value of 10e-150.
>
> Cheers,
>
> Ed.
>
> Cheers
>
>
>
> --
> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
> Julian, King of Lemurs
