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For newcomers

Find and download a net

From "what is a net" to a topology file on your own machine, in about twenty minutes.

This tutorial assumes you have met metal-organic frameworks but have never used this site. You will end up with a topology file on your machine and an understanding of what is in it. You need nothing installed and no account.

What a net is

A metal-organic framework is built from nodes joined by linkers. Strip away the chemistry — forget which metal, forget which molecule — and what remains is a periodic graph: points joined by lines, repeating in three dimensions. That graph is the net, and it is what this site calls a topology.

Nets have short three-letter names by convention: pcu is the primitive cubic net, the one that looks like scaffolding. Thousands of frameworks with wildly different chemistry share it.

Two things are worth knowing before you search.

Coordination number is how many edges meet at a vertex. In pcu every vertex has six. A framework built from a six-connected metal cluster and a linear linker will very likely be pcu.

Coordination sequence counts how many vertices lie one step away, then two steps, then three, and so on. For pcu it starts 6, 18, 38, 66. It is a fingerprint: two nets that look alike but differ somewhere will diverge in these numbers, usually by the fourth shell.

Step 1 — search by what you know

Open Search topologies.

If you know the name, type part of it into Net name contains and search. Substring matching means pcu also finds pcu-c, its catenated relative.

If you do not know the name but know the chemistry, use Coordination numbers instead. Suppose you are working with a paddle-wheel node that offers four connections and a linear linker that offers two. Type 4,2 and search. You get every net that has both a four-coordinated and a two-coordinated vertex.

That is usually too many. Tick …and no others. Now the results are nets with exactly those coordination numbers and nothing else — a much shorter list, and the one you actually meant.

Why some matches are missing. 3077 topologies are loaded here and 2443 of them are published and listed. The other 634 are held pending licence verification: they came from the RCSR archive alone, whose terms nobody has confirmed, so they are not published and are not listed. The results page says how many of your matches were held, and a held net's address answers 403 with an explanation rather than pretending it does not exist. A held net is one we hold and cannot serve, which is a different answer from "no such net". Licensing has the full position.

Step 2 — read a record

Click a name. Take pcu if you searched for it.

The page opens with the crystallographic description: spacegroup, cell lengths and angles, and the transitivity pqrs — how many distinct kinds of vertex, edge, face and tile the net has. 1,1,... means every vertex is equivalent to every other and every edge to every other. Low transitivity means a highly symmetric net, and highly symmetric nets are the ones frameworks tend to adopt.

Below that is one row per distinct vertex, with its coordination number, its site symmetry, its vertex symbol and its coordination sequence. This is where you check that the net really is the one you want: compare the coordination sequence against the one you computed, or against a published value.

Step 3 — take it with you

In the sidebar, Download:

  • .mfpx is the topology in the format the molsys tooling reads. Take this one if you are going to build a structure from it.
  • .xyz is plain coordinates, readable by almost anything.
  • .json is the record's metadata, the same content this page shows, for a script.

Try the JSON in your browser. It is the same address as the page you are on, with .json appended — every record works that way, and a program can also ask for it by sending Accept: application/json to the ordinary URL.

Step 4 — cite what you took

Under Cite this record is a citation block naming both the record's permanent URI and the dataset release it came from. Paste it into your notes now, while you know why you downloaded the file. The licence is stated right below it, per record — not one blanket statement for the whole site.

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