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

From: Jan-Philip Gehrcke <>
Date: Wed, 13 Jul 2011 15:08:15 +0200

On 07/13/2011 02:11 PM, David A Case wrote:
> 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.
> ...dac

Thanks a lot so far. I will see if the details you named hold true,
otherwise I will show up again. And of course I would be happy about
even more comments/opinions. Also, I think it would be nice to have this
behavior explained in an FAQ and/or in the docs.



Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universitšt Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Wed Jul 13 2011 - 06:30:04 PDT
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