[Wien] converting struct file into CIF formant
Fecher, Gerhard
fecher at uni-mainz.de
Sat Aug 28 15:52:44 CEST 2021
For your info,
the Kdist programm coming with the free Kalvados program suite (https://www.fzu.cz/~knizek/kalvados/)
reads and writes Wien2k struct files and can save them in different formats e.g.: cif
the cif has 8 digitsafter dot for the positions such that hexagonal cases are ok.
It allows a lot of manipulation of the structure, creation of superstructures, etc
Ciao
Gerhard
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."
====================================
Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz
________________________________________
Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von Laurence Marks [laurence.marks at gmail.com]
Gesendet: Donnerstag, 26. August 2021 10:48
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] converting struct file into CIF formant
Dear Gavin,
Unfortunately it is very possible to create problems by reducing the number of digits; Wien2k may not find the full symmetry.
I will mention a different code, Cryscon (http://www.shapesoftware.com/00_Website_Homepage/). It is shareware, so you are requested to pay a modest fee. In addition to converting struct to CIF with 8 digits, it will also transform axes and change symmetries which is really useful.
_____
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu<http://www.numis.northwestern.edu>
On Thu, Aug 26, 2021, 00:11 Gavin Abo <gabo13279 at gmail.com<mailto:gabo13279 at gmail.com>> wrote:
Prof. Marks,
Appreciate the warning and rhetorical questions.
I downloaded your "ct1c00630_si_002.zip" file at [1] and extracted 1x1.cif from it.
I opened it in the Windows 64-bit Edition of VESTA version 3.5.7 and exported it from VESTA as a .cif.
Indeed, that VESTA version takes the 8 places after the decimal point and truncates the atomic positions to 6 places.
I also uploaded the 1x1.cif in the Structure Data Converter & Editor of Bilbao Crystallographic Server [2] and it could not read the Symmetry Operations from the cif and truncated to 5 places.
For example, your .cif: Ti001 z=0.20224167
VESTA exported .cif: Ti001 z=0.202242
>From Bilbao's "Export to Standard CIF format" button: Ti001 z=0.20224
Should significant digits [2] be of concern, I will have to copy the value from StructGen for example and use a text editor [4] to adjust the exported .cif from those software programs. Or perhaps a software program like publCIF [5] or EnCIFer [6] would work instead of a text editor to edit the .cif. Or I could use WIEN2k's .struct to .cif converter command "x struct2cif" (or "x cif2struct" to go the opposite way) described in the WIEN2k usersguide [7] as you have already mentioned.
[1] https://doi.org/10.1021/acs.jctc.1c00630<https://urldefense.com/v3/__https://doi.org/10.1021/acs.jctc.1c00630__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpXftlM7Ng$>
[2] https://www.cryst.ehu.es/cgi-bin/cryst/programs/mcif2vesta/index.php<https://urldefense.com/v3/__https://www.cryst.ehu.es/cgi-bin/cryst/programs/mcif2vesta/index.php__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpUXrS6OPw$>
[3] https://en.wikipedia.org/wiki/Significant_figures<https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Significant_figures__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpU6sooZAw$>
[4] https://en.wikipedia.org/wiki/List_of_text_editors<https://urldefense.com/v3/__https://en.wikipedia.org/wiki/List_of_text_editors__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpV2G4zGEg$>
[5] https://journals.iucr.org/services/cif/publcif/<https://urldefense.com/v3/__https://journals.iucr.org/services/cif/publcif/__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpWDsd3Arw$>
[6] https://www.ccdc.cam.ac.uk/Community/csd-community/encifer/<https://urldefense.com/v3/__https://www.ccdc.cam.ac.uk/Community/csd-community/encifer/__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpU33r7mOA$>
[7] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf<https://urldefense.com/v3/__http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpXPqHimLw$>
Thanks,
Gavin
On 8/25/2021 6:35 AM, Laurence Marks wrote:
Sorry Gavin, but I would be very cautious about these versions. Do they preserve symmetry, and do they have 8 digits? Do they truly obey the CIF definitions? (struct2cif somewhat does).
_____
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu<http://www.numis.northwestern.edu>
On Wed, Aug 25, 2021, 07:32 Gavin Abo <gabo13279 at gmail.com<mailto:gabo13279 at gmail.com>> wrote:
See VESTA's website [1] on how it exports cif [2] and opens a .struct file.
CrystalMaker also has a "Import Data From: WIEN2k Structure" and "Export
Data To: CIF" according to its website [3].
[1] https://urldefense.com/v3/__https://jp-minerals.org/vesta/en/__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKL-f_jFpQ$
[2] https://urldefense.com/v3/__https://youtu.be/lxMbH71JvHA__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKKY62ZEnw$
[3] https://urldefense.com/v3/__http://crystalmaker.com/crystalmaker/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKJ4aeXwDg$
On 8/25/2021 5:56 AM, 413119008 at nitt.edu<mailto:413119008 at nitt.edu> wrote:
> Respected sir,
>
>
> Is there any way to convert a .struct file into .cif file
> format?
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