Re: [modeller_usage] Hybrid-36 Numbering Support in Modeller

[Modeller Caretaker <>]

On 2/25/19 11:25 PM, dms305 wrote:
> When using the complete_pdb.py script bundled with Modeller to complete 
> PDB 5GJQ, the resulting PDB model has more than 99999 atoms, which 
> leaves atoms with a numerical ID greater than this with IDs "*****" when 
> the PDB is written out to a file. Is it possible to enable hybrid-36 
> numbering support in Modeller so that these IDs can be used in 
> downstream analysis?

Sure, that's easy enough to add for atom serial numbers, and will be in 
the next release (although many programs, including Modeller and 
Chimera, ignore the atom serial number anyway). You'll still need to 
renumber residues (e.g. starting at 1 for each chain) otherwise you'll 
run into the same problem with residue numbers in the PDB file. That is 
less straightforward to fix though because Modeller's internal residue 
number has the same limits as the PDB format.

	Ben Webb, Modeller Caretaker
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