User-interface Documentation

CIFellipsoid

This is the main command line script for using PIEFACE to compute MBE from one or more CIF files. Details of the input parameters are given below, or by typing CIFellipsoid --help.

cifs

Name(s) of CIF files to import as a space-delimited list. Can also accept valid web address(es).

-m, --metal
Site label(s) (as found in the CIF file) of polyhedron centres to analyse (e.g. Fe1).
Most regular expressions can be used to make searching easier:
Al.*:matches any site label starting Al (Al1, Al2 ... Al9999 etc.)
Al?:matches any label beginning Al, but only 3 characters in length (e.g. Al1 - Al9)
Al[1-9]:matches any site Al1 - Al9
In addition to most normal regular expressions, preceding any label by # will omit it from the search:
#Al1:will omit Al1 from the list of acceptable centres.

By combining these terms, it should be possible to specify most desired combinations.

-o, --output

Name(s) of output files to save results to. Default is <CIF Name>.txt.

-r, --radius

Maximum distance to treat a ligand as part of a polyhedron (default 3 Angstrom).

-l, --ligandtypes

Types of atom (as specified by CIF atom_type) to be considered as valid ligands (can use regular expressions). Default is all atom types.

-n, --ligandnames

Atom labels to use as ligands (same syntax as –metal). By default, any ligand allowed by –ligandtypes is allowed. The combination of –ligandtypes and –ligandnames is taken as an AND-like operation, such that sites are only excluded if done so explicitly.

-t, --tolerance

Tolerance to use for fitting ellipsoid to points (default 1e-6).

-b, --phase

Name of data block to read from CIF file (default is first alphabetically)

--maxcycles

Maximum number of iterations to perform for fitting (default infinite).

-N

Don’t save results to text files

-W, --overwriteall

If existing results files already exist, force PIEFACE to overwrite them all.

-P, --PrintLabels

Print all valid site labels for each CIF file supplied.

-U, --Unthreaded

Turn off parallel processing of CIF files.

--procs

Number of processors to use for parallel processing (default all).

--noplot

Don’t produce interactive ellipsoid images after calculation.

--writelog

Write a debugging log to debug.log.

-V, --version

Print version information, check for updates, and exit.