Possibility to increase 'mapping-weight' of a certain atom

[ricalessandri]

It could be useful to have the possibility to increase the weight of an atom in a mapping, as sometimes we want to include only 1/2 atom in a certain bead.

Not sure what's the best way to implement it, but I can think of these possibilities:

right now the first click on an atom assigns to the current bead, while a subsequent click on the same atom removes it from the current bead. This could be modified in a way that by clicking again on an atom this does not get removed from the bead immediately but, at first, its weight on the current bead gets increased (this could be limited to a max weight of 3 I think): so the first click gives weight 1, the 2nd gives weight 2, the third 3rd 3, and the 4th click removes the atom from the bead
having some drop-down menu somewhere

[jbarnoud]

What output are you using and what are you feeding them to? I can allow custom weights and I can apply them to the GRO output, but for them to be useful I need to know how to express these weights.

Martinize2 has a syntax that should allow that, but I do not know if it is part of your pipeline.

[ricalessandri]

Currently I'm uploading mostly PDBs (probably poor formatted ones from the LigParGen server..) or GROs. And, while I download and store all output files - GRO, NDX, and MAP - the NDX files are the ones that I need to edit by hand if i want to use them with GROMACS to extract bonded parameters.

So, for example, in the NDX file an atom with weight 1/2 would be atom 2 in the following bead:

[Bead_1]
1 1 2 3 3