Daniel Beltrán

ValueError: unitcell angle < 0

9

Hi everyone, I'm getting this error (ValueError: unitcell angle < 0) when saving trajectories. It happens with different trajectory formats and it is quite random since sometimes it happens and...

Problem when transparent representations overlap

3

Hi :) I observed that when you look through a transparent (opacity < 1) representation you may not see other transparent representations. This happens even if the closest representation has...

RMSD perres ignoring ions

7

Hi, I just found out rmsd_perres is ignoring some ions (not always all ions). Those ions are an independent residue with 1 unique atom each. I can provide a pair...

New biomol fields

3

This is the third option on how to include biomolecular data within Optimade. This has been discussed in [issue 389](https://github.com/Materials-Consortia/OPTIMADE/issues/389). It introduces two new main fields: biomol_chains and biomol_residues. These...

new builtin package: ambertools

9

This package worked properly in a custom spack. However, I was not able to test it in the current spack due to a known [issue](https://github.com/spack/spack/issues/41146) with the python tkinter variant.

RuntimeError: error_theta is not one of the parameters [theta phi psi dx dy dz]

1

Hi David, I just installed tmscoring with "pip install tmscoring" First, it complained about the iminuit module to be missing so I installed it with "pip install iminuit" Now I...

Buggy $ref behaviour in paths

1

- OS: Ubuntu 18 - Browser and version: tested in Firefox 127.0.2 and Chrome 109.0.5414.74 - Method of installation: npm install swagger-ui-express - Swagger-UI version: Tested in 4.1.2 and 5.0.1...

Precentered is ignored when atom_indices != None

5

Hi everyone, I'm running a RMSD test in different regions in my structure to tell if there are jumps across periodic boundaries along the trajectory. To do so I need...

Problem with Trajectory.superpose

1

Hi everyone, I have been using the trajectory superpose function in my pipeline for a while. Now I'm having a new problem I never encountered before: the superposed trajectory has...

Broken link

1

Hi, In the [introduction](https://github.com/jamesaoverton/obo-tutorial/blob/master/docs/introduction.md) there is this link which is broken: [NCBITaxon](http://www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page) Best regards