When I open a CIF file in GaussView, I can see several molecules that form the unit cell. Opening the same CIF file in other pieces of software only visualises one molecule and draws the borders of the unit cell. On reading the file in a text editor I only see the coordinates for one molecule, so there is something that GaussView does to translate it across the unit cell.
Any suggestions for an alternative software that could also do this whole unit cell visualisation? A collegue does not have access to GaussView, so a free option would be nice.
Hi Maria Dimitrova,
I have understood your problem. Gaussview is not much popular in opening a crystal files. The XRD structure files are best when they are viewed using Mercury, which you can download freely from its CCDC website. Just type mercury download in google, you will be taken to mercury's home page there you can download its free version, which is much sufficient for structure elucidation and viewing.
Thank you very much, Venkatesan Ragavendran! It works just as I was hoping it to.
Just to complete this topic for other people that might be interested: What software works best depends on the type of crystal structure one wants to view. For small molecules I prefer MERCURY, too. For small inorganic structures, VESTA works best for my needs, as it allows easy definition of coordination polyhedra. Could anybody provide a suggestion for large-scale framework structures, like zeolites or MOFs?
In my view, VESTA is the best option, also for framework structures like zeolites or MOFs. The visualisation is quite fast, at least for reasonably sized unit cells (I don't think I have ever tried using it for MOFs with huge unit cells > 50 Å for each direction).
gdis could be an alternative that might be even more efficient for very large structures because the visualisation is a bit less sophisticated than VESTA (i.e. the pictures are not quite as nice).
Hi maria,
ITS very happy to hear that you have got your problem resolved. Keep going with your work progressing.
My best wishes.....
Mercury is good enough for upto 250 atoms' cif, ~50 Ang. At least I used it successfully to view and extract coordinated from cif.
However, gaussview is better at isolating the unitcell from the cif files. It wraps around the molecules within single unitcell, and this is useful in more than one cases.
I also observed that gaussview was better at detecting problematic cif files.
VESTA is another good option to convert between cif and different formats. One can directly get POSCAR from cif using VESTA, and it also provides fraction coordinates out of cif files.
StruMM3D is much better than Mercury, and will handle very large molecules. StruMM3D will handle many file types, including CIFs.
I see this 2015 question just now, and here I provide my solution to open a single crystal structure on Gaussian.
1. Clean your CIF(On Diamond) data, delete like a solvent, counter ion, or anything you don't want it.
2. Save your data as an XYZ file.
3. Open the XYZ file with ".txt" you'll see a list "Atom" "X" "Y" "Z". copy it.
4. Open Gaussian and casually create a molecule, store it.
5. Open that Gaussian file with ".txt". And you'll see "Atom" "X" "Y" "Z" also.
6. Delete that "Atom" "X" "Y" "Z" and paste your Own "Atom" "X" "Y" "Z". Store it.
7. Open the file you just modify. (With Gaussview)
8. Maybe you'll see the bonds are very chaotic. Don't worry, click on "rebond" and your molecule is ready to go!
All the best,
T.-L. Lee
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