Cell File Syntax

Software CrystFEL
1

I swear I found a page describing the .cell file syntax before, but for the life of me I can’t find it anymore. Can someone help me locate the docs for this?

2

Could this be? CrystFEL/relnotes-0.6.0 at master · biochem-fan/CrystFEL · GitHub

CrystFEL offers you the ability to index patterns using Bravais lattice
information but without unit cell parameters, for example: "index these using
only tetragonal primitive lattices, but any parameters".  However, it's awkward
to give this information using a PDB file: you essentially have to "trick" it
into interpreting the parameters correctly, then throw away the parameter
information.

Version 0.6.0 of CrystFEL introduces a new way of specifying unit cell
information.  These new unit cell files look like this:

         CrystFEL unit cell file version 1.0

         lattice_type = cubic
         centering = I

         a = 66.2 A
         b = 66.2 A
         c = 66.2 A

         al = 90.0 deg
         be = 90.0 deg
         ga = 90.0 deg

In the event that you want to specify the lattice type information alone, you
can simply omit the cell parameters:

         CrystFEL unit cell file version 1.0

         lattice_type = tetragonal
         centering = P
	 unique_axis = c

Note that a unique axis must be specified for all types of cell where this makes
sense, and can be omitted otherwise.  This was done in the first example above,
which is cubic and therefore has no unique axis.

You can, of course, continue to use PDB files just like before.
3

certainly has the info i was looking for, thanks! i think there’s probably a more official source than the release notes though.

4

You’re right, this is a bit of an oversight in the documentation. I’ll add it somewhere sensible shortly (unless someone wants to send me a patch..), e.g. in man crystfel or man indexamajig.

5

no worries, @taw. it’s a pretty sensible syntax. i was able to figure it out for my dataset, but adding a page would be nice. naive question – do i need a desy account to send a PR to the desy gitlab? doh answered my own question. didn’t realize there was a GitHub page too.

6

i put in a PR: Unitcell man page by kmdalton · Pull Request #25 · taw10/crystfel · GitHub. claude did the first draft so it might be a tad verbose, but i suppose that’s better than not verbose enough.