Re: [Jmol-users] PDB format replacement

[Robert H. <ha...@st...>]

On Wed, Jan 28, 2015 at 11:33 AM, Rolf Huehne <rh...@fl...>
wrote:

> Hi all,
>
> I am looking for a replacement for the PDB format that offers the same
> options like predefined atom numbers, atom names, residue names etc.
> after loading into Jmol. But without the restrictions of the PDB format
> regarding atom count and residue number count.
>
> Q: Is there anything other than the (horrible) mmCIF format that Jmol
> can read and interpret similarly to the PDB format?
>
>
I think if you believe mMCIF is "horrible" then you should look again. You
can
basically put a standard PDB file straight into it with a simple header
that identifies
the fields. What could be easier than that? -- Same data used twice, though
you
do need a space character between alt-loc and insertion codes in mmCIF.

Why is this "horrible"? Maybe there is so much information in the RCSB
files, but
Jmol doesn't need more than this:

data_3J06

_database_PDB_rev.num 1

loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id

ATOM 1    N  . ? -70.914 -42.745 -13.483 3 SER A N
ATOM 2    C  . ? -69.991 -43.612 -12.692 3 SER A CA
ATOM 3    C  . ? -68.548 -43.499 -13.189 3 SER A C

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