Daniel Beltrán comments

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                                            Daniel Beltrán

Problem when transparent representations overlap

I see. Thanks for your reply :) It won't be easy changing to molstar since NGL is deeply integrated in our project, but I think one day we will have...

RMSD perres ignoring ions

I attached 2 pdb and 2 xtc trajectory files. In the first example there is only 1 zinc atom. it is the penultimate residue in the pdb. Run this code...

Support for SMARTS filter language (`filter_smarts`)

Sorry, I have no experience with SMARTS

Using OPTIMADE for Biomolecular data

Hi everyone, My name is Dani and I am the technician from Adam Hospital's group who is going to implement the OPTIMADE specifications in a biomolecules database ([BioExcel-CV19](https://bioexcel-cv19.bsc.es/#/)). I have...

Using OPTIMADE for Biomolecular data

Hi Johan, > Perhaps we can also use a shorter prefix like bio or biomol. It looks even better to me. > I mostly placed the mass and chemical formula...

Using OPTIMADE for Biomolecular data

Hi Andrius, > I think limiting chain name to a single character is too restrictive. However, if the plan is to stay compatible with the PDB format, then it makes...

Using OPTIMADE for Biomolecular data

> We could add an atom_count field, in that case it would however require a clear definition of which atoms should be counted and which not. E.g., would atoms of...

Using OPTIMADE for Biomolecular data

> Would the nsites field be sufficient for this? Totally > There are two ways in which you could handle a changing number of atoms. Perfect > Using the first...

Using OPTIMADE for Biomolecular data

Last Friday meeting @sauliusg pointed that we were not handling atom names with the new biomol fields. Then @JPBergsma suggested that we could handle them with the species 'original_name' property....