dkratzert / finalcif Goto Github PK

• The text editor after file saving should show the CIF with line numbers

_computing_structure_solution 'isomorphous replacement'
_atom_sites_solution_primary isomor

creates:
The structure was solved by isomor methods with isomorphous and refined by full-matrix least-squares methods against F2 using SHELXL-2018/3.[3,4]

And references are incomplete:

[1] Bruker, SAINT, V8.40B, Bruker AXS Inc., Madison, Wisconsin, USA.
[2] L. Krause, R. Herbst-Irmer, G. M. Sheldrick, D. Stalke, J. Appl. Cryst. 2015, 48, 3–10, doi:10.1107/S1600576714022985.
[3]
[4] G. M. Sheldrick, Acta Cryst. 2015, C71, 3–8, doi:10.1107/S2053229614024218.
[5] D. Kratzert, FinalCif, V118, https://dkratzert.de/finalcif.html.

Probably a list of cif keys (not currently used in loops) with a, "append" button.

Append will create a loop and more rows can be added as usual.

There could be also a "add column" button?

Pro:

• Easier to understand what you need to fill in
• Works again with templates from before V115
• More flexibility about the first half-sentence like "The compound was crystallized "

Contra:

• Repetition of the same half-sentence in each template

Anything else?

Probably, there is no conversion of special characters in the dropdown menus?

Sopport multiple machine templates in one CIF for a site configuration with multiple diffractometers

I am building FinalCif v113 and running its tests on Debian unstable. Some of the tests appear to hang indefinitely. It is difficult to pinpoint which of them exactly: at first it appears to be the tests in tests/test_workfolder.py, but if I disable it, hang happens earlier (!), most likely at tests/test_options.py.

Debian test system disallows network access (and sets NO_NETWORK=1 in environment, as discussed earlier), and it also forbids reading/writing in user's home directory. If hung tests need read/write to user's home directory, I can enable that, but I need to know how these directories are accessed. I tried using XDG or HOME environment variables, but they do not seem to work.

Clarify that some are hard-coded, but can be overridden by a new definition

• Create ADP table
• Add option for ADPS in options page
• Add ADPs to template docs

FinalCif should save a diff to the original CIF in the work directory in order to keep the changes made by the user.
How to select which changes to keep? We don't want to keep atom parameters for example.

• Probably only changes edited by templates?
• Or should I add checkbox to the text temlates where you can activate "keep this thing"?

• Input form for squeezed void (solvent etc)
• check for .fab (ABIN) file
• what else?

_publ_section_references needs a possibility in the GUI to select one or more items of a references list and combine the to a string. I don't want to make FinalCif be a reference editor.

Add ability to generate multi-tables from a word template

• Description of twinning
• Test more types of twins
• Add twin matrix to the structure report.
• What else?

It should instead show a warning where the invalid character is located and exit gracefully.

Add citations to checkcif and validation response to the documentation.
Add citations section to documentation for all other software.

Add a central button to export all templates for equipment, dropdowns and text editors to a single file.
Location will be in options page.

Add an indicator (symbol?) what kind of report is generated hard-coded or templated.
Probably add "from template" to the button text if a template is chosen.

Refinement using NoSpherA2, an implementation of NOn-SPHERical Atom-form-factors in Olex2. Please cite: F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021 NoSpherA2 implementation of HAR makes use of tailor-made aspherical atomic form factors calculated on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF wavefunction - either Hartree-Fock or DFT using selected funtionals - for a fragment of the crystal. This fragment can be embedded in an electrostatic crystal field by employing cluster charges or modelled using implicit solvation models, depending on the software used. The following options were used: SOFTWARE: ORCA 5.0 PARTITIONING: NoSpherA2 INT ACCURACY: Normal METHOD: PBE0 BASIS SET: def2-TZVP CHARGE: 0 MULTIPLICITY: 1 SOLVATION: Chloroform DATE: 2022-07-22_17-00-22

• Add citation of F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C to FinalCif
• Format the "The following options were used:" paragraph properly (newlines)

“The structure were solved by dual method" should be "... was solved ..."

Add the possibility to save collections of validation responses.

revert changes does not work after move up/down

I don't like them, but people are using them.

• Add a dropdown menu to select the current cif
• Disable data sources for multi cifs
• show data name in the response forms list
• use data name in response forms list to save it to the correct cif block

• do not write an empty changes file
• do not complain about changes if the file contains only a _data entry

The atom table in the report document is empty.

Adding of
“H"ubschle, C. B., Sheldrick, G. M. and Dittrich, B. (2011). J. Appl. Cryst., 44, 1281--1284.”
does not work? What happens to the \"u ?

How about & and " characters?

Would it make more sense to store the info in FinalCif under _audit_author_address instead of _audit_contact_author_address?

The CSD removes most of _audit_contact_author_address and all other audit_contact_author[] fields.

Pros

• The information would not get lost. Most of the needed UI work is done already.

Cons

• Way more complicated input of CIF author information.

Rearange buttons to save author templates. The button to save the current author to the templates should be moved left. The button is too easy to miss.

“with a fine focus sealed tube X-ray source using a Triumph curved graphite crystal as monochromator

Solution:
Get name of *_0m.raw file and use name of * for the base name of the file search for all other files.

The references are at the end of each sentence. Wouldn’t it be better to have them directly after each piece of software?

Test if windows 8 works

The geom[]_publ_flag code signals whether the angle is referred to in a publication or should be placed in a table of significant angles.

• Make an extra table of these bonds/angles in the report.

Example:
no do not include angle in special list
n abbreviation for "no"
yes do include angle in special list
y abbreviation for "yes"

I am thinking of a larger widget for the template editor at the place of the main table, like the loop editor.
Each template could have an extra option for short text (dropdown menu) and long text: "Long text" would mean that the templates are not edited by a dropdown but a popup widget with a full-featured text editor.

The file open dialog does not go to the last directory anymore

Currently, the order of author can not be changed.

Pro:

• Wording gets difficult and the current order is not optimal
• Values are already in the table

Contra:

• Text is more 'complete'

Anything else?

While looking at the code, I noticed calc_checksum function to calculate SHELX cheksums:

Thus I am interested in the reference for this function, as I was unable to find SHELX checksums explained in SHELX manuals. Could it be that checksum algorithm has changed at some SHELX version? This could explain ~6% mismatching SHELX data in the COD.