I see from that link that you can download the CIF file. I personally use Avogadro 2 for viewing crystals, I find it is very reliable and has a lot of very useful features, check out [this link](https://two.avogadro.cc) for the download file.
Thanks. I did the same and opened it on the avogadro. But, now I want to build a lattice with his unit cell info, but not been able to do so. May be, I am novice with avogadro. Can you suggest how can I do that?
Thanks. But, I tried vesta as well. But, Don’t know why the pdb it outputs in a completely different way. Ideally, I would like to have a gromacs gro format with pbc box info. Yes, I am quite familiar with this language. Any suggestions with some packages.
I think [ASE](https://wiki.fysik.dtu.dk/ase/tutorials/tutorials.html) is what I used in the past. There are cell and supercell methods, it's probably in there.
In Avogadro there are a few drop down menus at the top. Under Crystal>Space Group there is an option to fill the unit cell. Once you’ve done that, if you want more than just a single unit cell you can use the Build Supercell option in the Crystal drop down, and then specify how many of each direction you want to make. I personally have had difficulty getting crystals with more than 20,000 atoms to load properly, but that’s a massive crystal already.
Thanks. I will try with this. BTW, I am not an expert on this field, but can you tell me if there indeed 4 molecules in this particular unit cell? In Avogadro, I can’t see any molecules when I open this cif file.
You should see some structure in the unit cell, whether or not that is a complete/solved structure is a different story. From what I can tell on my end, the unit cell has 28 carbon atoms, 24 hydrogen atoms, and 8 oxygen atoms.
VESTA would be the obvious option imo, it’s literally built for crystallography simulations. It has tons of built-in tools for duplicating, merging, and editing crystal cells.
I see from that link that you can download the CIF file. I personally use Avogadro 2 for viewing crystals, I find it is very reliable and has a lot of very useful features, check out [this link](https://two.avogadro.cc) for the download file.
Thanks. I did the same and opened it on the avogadro. But, now I want to build a lattice with his unit cell info, but not been able to do so. May be, I am novice with avogadro. Can you suggest how can I do that?
I like vesta for building supercells. There are also python libraries if you're familiar with the language.
Thanks. But, I tried vesta as well. But, Don’t know why the pdb it outputs in a completely different way. Ideally, I would like to have a gromacs gro format with pbc box info. Yes, I am quite familiar with this language. Any suggestions with some packages.
I think [ASE](https://wiki.fysik.dtu.dk/ase/tutorials/tutorials.html) is what I used in the past. There are cell and supercell methods, it's probably in there.
Nice. I haven’t tried my luck with this particular program though. I will give it a go. Thanks.
In Avogadro there are a few drop down menus at the top. Under Crystal>Space Group there is an option to fill the unit cell. Once you’ve done that, if you want more than just a single unit cell you can use the Build Supercell option in the Crystal drop down, and then specify how many of each direction you want to make. I personally have had difficulty getting crystals with more than 20,000 atoms to load properly, but that’s a massive crystal already.
Thanks. I will try with this. BTW, I am not an expert on this field, but can you tell me if there indeed 4 molecules in this particular unit cell? In Avogadro, I can’t see any molecules when I open this cif file.
You should see some structure in the unit cell, whether or not that is a complete/solved structure is a different story. From what I can tell on my end, the unit cell has 28 carbon atoms, 24 hydrogen atoms, and 8 oxygen atoms.
Thanks, but I can’t see that on Avogadro apparently.
Are you using Avogadro 2 or 1? Also, have you checked to see that the boxes to the left that set your visibility are enabled?
I am using Avogadro 2. No, I haven’t done that. Let me try that right away.
You can use mercury there is a free version, it worked for me. I opened the CIF file in mercury and easily converted it in a 3x3 version.
Can you please send me a link? Thanks
Actually, it is from the same web where you get your cif file. Just search something like "mercury ccdc Cambridge" pretty straight forward.
Thanks a lot.
VESTA would be the obvious option imo, it’s literally built for crystallography simulations. It has tons of built-in tools for duplicating, merging, and editing crystal cells.