cryos
Crystal structure builder duplicates atoms
Greetings. Your program is really fantastic thanks for all your hard work.
Here is the bug: When I enlarge the C axis using the super cell builder on molecules such as the one attached, the resulting structure has duplicate atoms. You can check by using the attached file (I got atom positions from paper: Imberty 1988 Biopolymers v27 p1206) and build up the c axis in super cell builder (aka make c=1 and generate) and you can see if you select rings or if you look in cartesian editor that there are some atom duplicates. This occurs because there are slightly more atoms in this basic structure than should be in one unit cell, so those get duplicated. I have found no solution to this other than random cutting, or using excel to easily find duplicates and erase them. It would be great if you put in a routine to get rid of duplicate atoms, either in the cell builder or seperately.
Thanks so much.
Reported by: *anonymous
Starch Helix type B transcribed from Imberty 1988
Original comment by: nobody
I can confirm this and it looks like the supercell extension should be removing duplicates already? Marcus, any ideas here?
Original comment by: @dlonie
Sorry for the delay. I'm taking over the supercell generation feature, so I'll check this bug before the 1.1 release.
Original comment by: @ghutchis
I just wanted to note that this bug is still there in Avogradro 1.2.0. It can be reproduced as follows:
- File/Import/Crystal/C-graphite
- Build/Super Cell Builer ...
- Enter multiplicity 10x10
- export file as .CML
The resulting file should have 400 atoms, but it has 500 atoms. If I copy paste the individual layers, I find that the lower layer has 200 atoms, the upper layer has 300 atoms.
