creating and visualising pdCIF files

rowlesmr

Hi all

My paper on visualising pdCIF data is out. Is open access, so hop on over:

https://doi.org/10.1107/S1600576722003478

If you'd like to be able to more easily share your data and results, then pdCIF is an option for you. With this program you can view any (compliant) pdCIF and see what the end result of a refinement was. I've also put together a bunch of macros to make it easier to output pdCIF from TOPAS refinements.

The macros are available as SI on the paper, or on the user macros: http://topas.dur.ac.uk/topaswiki/doku.php?id=out_pdcif

There is information on how to get my program in the paper, as well as a stand-alone windows version, here: https://www.iucr.org/resources/commissions/powder-diffraction/projects/pdcif

Hope this is helpful to all.

Matthew

johnsoevans

Finally the most frequently asked question on the forum is answered! And answered superbly!

Many thanks Matthew for the work here and for sharing all the macros. It's going to be useful to so many people.

mathiasmorch

Hi Matthew,
Thank you so much for the macros, they're really useful!
I have a small problem that i haven't been able to work out on my own, that means the output files don't directly read into the plotting script.
When outputting the bond angles there's not always sufficient spacing between the angle and the symmetry code.
A snippet of two lines looks like this:

	O1_S      O1_S      O1_S       60.000  101_775 1_555  78_577
	O1_S      O1_S      Fe2_S      47.88(4)101_775 1_555  51_776

I have tried changing around

	Out_CIF_newfile(ciffile)
	consider_lattice_parameters
	Out(Get(cif_bonds_angles), "%s")

To various settings:
Commenting out "consider_lattice_parameters"
Trying to specify the string length "%s100"
Adding tabs "\t%s"

To me it doesn't seem like any of these options are passed.
I don't know if this is because the "Get(cif_bonds_angles)" command just returns one big string block with all the information? And i haven't found any hints to whether it is possible to pass any formatting arguments to Get()?

Alternatively i don't know if it's possible to give any flags to ReadCif so this parses correctly?

rowlesmr

Hi Mattias

Yes, Get(cif_bonds_angles) just returns a giant pre-formatted string.

What version of TOPAS are you using? This looks like a TOPAS bug. If you can share, are you able to send me your data and input file so I can have a play?

Two ways I can think of to work around it:
1) don't use do_errors (Not a great one, I know)
2) do a search/replace on the CIF file: /(\d\))(\d)/$1 $2/ -> look for a digit followed by a closing parenthesis followed by another digit. Put a space after the parenthesis and before the final digit.

.

There aren't any flags, as "47.88(4)101_775" is a perfectly valid data value, it just isn't semantically valid, and so the parser can't tell the difference; we need to change the source before it gets there.

Matthew

rowlesmr

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