For researchers

File formats

What .mfpx is, what you get in .json, and which format to ask for.

.mfpx

The canonical deposit format, owned by molsys. It carries what a plain coordinate file cannot: connectivity, atom types, fragment assignment and cell information in one file. Nets, building blocks, fragments and framework structures are all stored as .mfpx.

Coordinates in an .mfpx are Cartesian, in ångström, not fractions of the cell — molsys keeps them that way and converts on demand. Reading them as fractional is a mistake that produces a plausible-looking structure at the wrong scale.

Read it with molsys:

import molsys
m = molsys.mol.from_file("pcu.mfpx")

Or fetch it straight into a mol object:

from mofplus import user_api
m = user_api().get_net("pcu", out="mol")

Atom types in an .mfpx may carry two annotations that matter:

• @ separates the atom type from its fragment: c3_c2h1@ph.
• % marks an annotated position within a fragment, used when depositing fragments whose parameters depend on which position is which.

.xyz

Plain coordinates, no connectivity, no cell. Present on records that have one, for use in tools that cannot read .mfpx. Do not use it as your archival copy: the connectivity is the part that took work to establish, and it is exactly what .xyz throws away.

The net viewer on this site does not use it — it reads the topology, so that the edges it draws are the edges the deposit records, periodic images included.

.json

The record's metadata, at the record's own address. Field names match the REST core. Every JSON record carries:

• uri — the permanent identifier
• licence — an SPDX-style identifier, never absent
• citation — a ready-made citation block, the record URI and the dataset release
• files — where the deposited files are

It is served both by appending .json and by sending Accept: application/json to the ordinary record URL.

.cif

Not currently served. Frameworks with published crystal structures are the obvious candidates; it is not offered rather than offered as a lossy conversion nobody checked.

Which one to take