The PDB format only allows 5 digits for the atom serial number, so something has to give once you get to the 100,000th atom. You must be using an old version of Chimera because the behavior you describe is what Chimera used to do — fill the field with asterisks. The current version of Chimera switches over to using “hybrid-36” numbering (described here) when it gets to the 100,000th atom.

According to wwPDB: Preparing PDBx/mmCIF files for Depositing Structures Large and Small, it looks like the PDB should accept hybrid-36 numbering, though they prefer mmCIF files. Chimera cannot write mmCIF files, but ChimeraX can. You don’t describe what processing you are doing in Chimera that makes this all necessary, so I don’t know if ChimeraX will be able to do all the other things besides writing the file that you will need. You could go over to www.cgl.ucsf.edu/chimerax and see if it looks like it does or not (the User Guide link probably being particularly useful for that).

—Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Oct 23, 2019, at 8:33 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:

Hello,

I'm trying to deposit a PDB with 50 chains. My PDB has a lot of HETATM
records and at some point it switches from HETATM"number" to
HETATM*****.

The PDB throws an error regarding HETATM*****.

If you any suggestions regarding the error and / or processing the
.pdb to make the deposition easier, please let me know. I also wonder
if I can save my file as a cif by Chimera.

Regards.
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