I am currently modifying my parser (for now all calculations and result data are in run folder because none of the default results sections fit into my data).
Can NOMAD recognize protein if I write protein coordinates in Result section? By that I mean to draw protein in New Cartoon representation and to color chains with different color (like it can be done in VMD or Pymol).
If so, can you please share few lines of code how to do it?
Second question is can NOMAD recognize coarse-grained structures, i.e. if I load them into results/structure section will NOMAD draw them on input page (because coarse grained structures will not contain any standard atom names).
Thanks for the question. At the moment, we do not have the feature for cartoon representations or for properly handling coarse-grained systems. But we do want to extend to the soft-matter realm, so these are relevant features that could be added.
I think the easier feature would be the cartoon representation: we use NGL to view the structures, and it has a built-in cartoon representation that could be toggled. Maybe we automatically enable the representation if certain criteria are met, or would we simply allow the user to switch the representation on-demand. Would you be able to send us a small example of the type of data you are thinking about? We could use it to prototype this.
The harder feature would be the ability to handle coarse-grained models. We have had some preliminary discussions about this, but there are no concrete plans or ideas on how to proceed. Once again it would be super helpful if you could e.g. send a small example of such data.
I saw that for some DFT calculations people have drawing of some small molecule on front page (for example benzene or some crystal). I don’t know what kind of code in parser I would need to get those drawings with my own parser.
I have attached you all-atom PDB structure of protein, all-atom PQR structure of protein, and coarse-grained structure of protein. I also have coarse-grained structures of proteins with Martini or SIRAH force field.
In general, VMD or Pymol can draw structure of proteins by choosing to color by residue name, atom name, secondary structure, chain name. In new cartoon representation, new ribbons etc. It can also draw easily coarse-grained structures because VMD doesn’t care if atoms/beads are called “H, N, O” or “XX, ZY, NY” and so on.
Same about residue names. For coarse-grained structures it can be also choose representation “VdW” with possibility to increase radii so beads will look larger than atoms.
We will look into the cartoon representation, I think it should be an option that the user can toggle.
I saw that for some DFT calculations people have drawing of some small molecule on front page (for example benzene or some crystal). I don’t know what kind of code in parser I would need to get those drawings with my own parser.
Do you mean something like this? This visualization that is shown is an interactive 3D view of the structure that has been extracted from the calculation. When we encounter a calculation that we can parse, we extract the contained structures and can then show a visualization for them.
If you are writing your own parser for computational data, then you should populate the data in run.system.atoms. This way our tools can pick up on it and also show it in the entry overview. Note that there are also other requirements that have to be met before a valid overview page can be shown. If you have any other problems with this, you could send us some example code/data to look at.