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

wkadlo via molmodel%40net.bio.net (by gkowadlo At gmail.com)
Mon Nov 27 04:55:57 EST 2006


hi, thanks a lot for taking the time to reply with that very helpful
advice and script.
i'll give it a go! :-)


Raoul Fleckman wrote:

> On 2006-11-27, Raoul Fleckman <raoul.fleckman At gmail.com> wrote:
> > On 2006-11-27, wkadlo <gkowadlo At gmail.com> wrote:
> >
> >   # ----  here alter stuff with the fields (most likely: $asn and $rsn)
> >   #
> >   # for example, if the unchanging part of the protein ends with its
> >   # final residue number ($rsn) equal to 197, then you want to replace
> >   # the $rsn below with "$rsnx++" and initialize it before the above
> >   # "while(<>) {" with "my $rsnx = 198"
> >   # ... and quite similarly for the atom sequence number ($asn)
> >...
>
> bad form replying to myself... but the residue number needs to be set as
> an increment not on each line as i indicated here, but rather as an
> offset of whatever the input is: "$rsn += xxx"; where "xxx" will change
> to old residue sequence number to one beyond the last one seen in the
> constant part of the protein listing.  ...sorry about that.  again, good
> luck.



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