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

Raoul Fleckman via molmodel%40net.bio.net (by raoul.fleckman At gmail.com)
Fri Nov 24 12:54:23 EST 2006


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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