[Molecular-modelling] Re: protein graft, pdb cleanup

wkadlo via molmodel%40net.bio.net (by gkowadlo At gmail.com)
Sun Nov 26 20:50:27 EST 2006


I did the grafting with a hypothetical protein in the program Discovery
(Accelrys).
so i have all the 3D coordinates, but the numbering in the file is
wrong (each fragment has retained the numbering from the original pdb's
that they came from).



Raoul Fleckman wrote:
> On 2006-11-24, wkadlo <gkowadlo At gmail.com> wrote:
> >
> > i have grafted a cap of a protein onto another uncapped protein, and
> > now the pdb file is not consistent.
> >
> > i am about to write a perl script to fix up the numbering and remove
> > the redundant terminus.
> >
> > are there already tools to do such a thing?
>
> there might be such a script available, but that would depend greatly
> what you mean by "grafted".  it's not clear if you did that grafting
> at the petrie-dish or the in-silico level. and if it is small change,
> (oh, let's say less than 25 residues), it might be easier, and even
> less error-prone to just perform that edit once in an editor.
>
> if you didn't perform this graft at the petrie-dish level (followed by
> a new structural data set), how do you know the new xyz coordinates?



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