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

wkadlo via molmodel%40net.bio.net (by gkowadlo At gmail.com)
Tue Nov 28 19:32:04 EST 2006


thanks again, that was really helpful, and improved my perl as well.


wkadlo wrote:
> 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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