Re: [AMBER] When and how is leap re-numbering residues?

From: David A Case <>
Date: Wed, 13 Jul 2011 08:11:55 -0400

On Tue, Jul 12, 2011, Jan-Philip Gehrcke wrote:
> What irritates me that in a work flow there may be at least three
> different numbering schemes:
> 1) the residue numbering from the original PDB file
> 2) the leap-internal residue numbering _directly after_ invoking `loadpdb`
> 3) the numbering of PDB files written by leap after invoking `savepdb`

This is indeed annoying.

For number 2), I think you can use the "desc" command to see what LEaP does;
my recollection is that it adds some large number to the "real" residue
number of chains beyond the first one.

For number 3), the final residue numbering is indeed sequential, with no gaps.
I believe that LEaP reorders chains in descending order of size (largest
chains first). I vaguely(?) remember there being some code that could turn
that reordering off, or maybe that has already been done. I'm mainly posting
this in case it jogs someone's memory who can supply more info.


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Received on Wed Jul 13 2011 - 05:30:02 PDT
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