I found an easy way of generating one molecule, a unit-cell or more. I open my CIF file with CCDC’s Mercury software (limited version is available for free on their website) and then save this file in PDB format which can then be open by Blender. The advantage is that Mercury generates as many atoms as seen on screen and not only symetry independent atoms.

I will try to adapt the part of your script where you draw bonds for polyhedra representation.

Cheers,

Erwann

The easiest way is always to convert a cif file to p1 symmetry, removing the need to infer symmetry. Most crystallographic programs will do this for you. If you don’t want to do that, OpenBabel does support inferring unit cells (OBUnitCell.FillUnitCell() – http://openbabel.org/dev-api/classOpenBabel_1_1OBUnitCell.shtml#af5cee9c530db13a5ec558a3783893315). You can write your own cif parser, but I have found that literally interpreting symmetry_pos_as_xyz causes issues due to poor regulation of experimental cif file data.

Good luck!

As a small molecule crystallographer I mainly work with the CIF file format and it would be fantastic if a Blender script could give the ability to act as a molecular builder with the atomic positions and symmetry elements given in the CIF file (I haven’t seen anything that could handle symmetry operations properly yet).

Also the ability to draw polyhedron around selected atoms would be awsome…

Anyway thanks for this tutorial which helped me understand quite a few things concerning python programming.

luckily, I managed to figure out the bug: There are mol2 files, which denote aromatic bonds with the number ’4′ as opposed to the ’2′ for the actual double-bonds. In this case, the above code unfortunately fails to produce the wanted output. After specifically setting them to conjugated double bonds rather than aromatic ones, everything worked fine for me

Thanks again & cheers,

K

I’m glad you’re following through with this! I’ve been meaning to update this blog post for a while now, as it doesn’t reflect changes I’ve made to the process over the last year or so. Have you looked at the github repository? It uses more generalized / faster code, has been updated to include changes to Blender over the last year, and, most importantly, should be easier to understand.

Edit: I updated this tutorial. The github version still deviates in how it handles blender meshes (using bpy.ops.* is slowww), but its conceptually aligned with this tutorial.

“bpy.ops.transform.translate(value=Vtrans[i])”

I always get the message that there was an error, yet, there is none specified in the console (I launch the code itself from a text editor window open in Blender as well)

I’ve tried printing out the Vtrans values to see, if there was something wrong with the file I’m using, yet, this gives me an ‘invalid syntax’ exception

Any ideas on what I’m doing wrong here?

Cheers & thanks,

K