Re: [ccp4bb]: Deleting by Chain ID

[Paul Hubbard <phubbard@post.its.mcw.edu>]

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Hi,

Thanks for the response. However, I would like to delete while viewing the
PDB file, as I am looking at a electron density map - and there are alot of
overlapping helices fit into the density (I want the best of the bunch). It
would be much easier if I could do it on the fly.

Thanks

Jeff Taylor wrote:

> How about :
>
> cat structure.pdb | awk '{ if ($5!="A") print $0}' > new_structure.pdb
>
> change the "A" to whatever chain ID you want to delete.  Also, change
> "awk" to "gawk" if needed.
>
> - Jeff Taylor
>
> --
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> Dr. Jeffrey S. Taylor       Duke University Medical Center
> Department of Biochemistry  Box 3711, Nanaline Duke Bld
> Phone (919) 681-5266        Durham, NC 27710
>
> Paul Hubbard wrote:
>
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > Hi,
> >
> > I am looking at an output file generated by FFFEAR, where lots of
> > potential helices are written to a PDB file. Each helix candidate is
> > written with a different chain ID. I would like to jump to each
> > consecutive chain, then delete the whole chain in one go if I don't like
> > it.
> >
> > My question is, what's the best way to do this. I have played with XFIT,
> > and can't seem to do it there except by deleting 1 residue at a time.
> > I've also looked at writing an O macro, but wild cards don't work - and
> > there's no symbol for last picked chain. Ideas gratefully accepted.
> >
> > Thanks
> >
> > AGS
> >
> > --
> > Paul Hubbard
> > Dept. of Biochemistry
> > Medical College of Wisconsin
> > Phone: 414-456 4305
> > Fax: 414-456 6510
> > URL: iris9.biochem.mcw.edu

--
Paul Hubbard
Dept. of Biochemistry
Medical College of Wisconsin
Phone: 414-456 4305
Fax: 414-456 6510
URL: iris9.biochem.mcw.edu