AMBER Archive (2002)

Subject: RE: Antibody residue numbering

From: Mark Hsieh (hsieh_at_abmaxis.com)
Date: Mon Aug 19 2002 - 20:00:03 CDT

Thank you.

I wrote a quick and dirty perl script to work around this.
It re-numbers the residues so that they are sequential and
contiguous within each chain. If anyone is interested
I can post the script.

Mark

> -----Original Message-----
> From: David A. Case [mailto:case_at_scripps.edu]
> Sent: Monday, August 19, 2002 2:16 PM
> To: Mark Hsieh
> Cc: amber_at_heimdal.compchem.ucsf.edu
> Subject: Re: Antibody residue numbering
>
>
> On Mon, Aug 19, 2002, Mark Hsieh wrote:
> >
> > Is there a way for tleap to correctly read in antibody PDBs
> > residue where the numbering includes a letter after the residue
> > number (e.g., 100, 100A, 100B, 100C, etc.)?
>
> Not using the usual definition of "correctly" :-)
>
> tleap will split the above residues into individual ones, but then the
> numbering won't match the input pdb file. And if 100A and 100B are both
> the same residue type (e.g. both ALA, etc.), tleap may not work
> at all, since
> its algorithm for figureing out where one residue ends and next
> begins will
> fail.
>
> Finding a way to preserve original residue numbers from a pdb file is on
> the list of things we are hoping to include in the next release.
>
> ..dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>