search

cryos / avogadro

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
http://avogadro.cc/
GNU General Public License v2.0
332 stars 155 forks source link

Fills Unit Cell Incorrectly #927

Open ahyork opened 4 years ago

ahyork commented 4 years ago

When I read in a structure in non-P1 symmetry and then use the Super Cell Builder feature and replicate out to 2x2x2, it doesn't convert to P1 symmetry correctly.

I found this when my mentor pointed out the overlapping CO2 groups that appear on the edge of the unit cell. I converted the structure to P1 symmetry using OpenBabel and compared to the super cell in Avogadro to double check and they were not the same structure.

I am running Avogadro 1.2.0 on Linux Mint 19 I attached the two files I was having trouble with below. They are .cif files but github won't allow that file extension.

KAXQIL_clean_P1.txt is the non-P1 structure file that is converted to P1 incorrectly in Avogadro

KAXQIL_clean.txt is 'KAXQIL_clean.cif' after it has been converted to P1 using the OpenBabel command obabel -icif KAXQIL_clean.cif -ocif -O KAXQIL_clean_P1.cif --fillUC strict in the command line.

Thank you for your help in advance!

ghutchis commented 4 years ago

Thanks for the bug report. That's strange - the tolerances are probably better in OB - although it's supposed to be the same code. I'll see what I can do, but I'm more likely to fix this in http://github.com/openchemistry/avogadrolibs for 2.0.