ValueError: could not convert string to float

[kexul]

When specify an ref ligand with it's ID in pdbbank , this error occured: ValueError: could not convert string to float: 'I1'.
Here is the code to reproduce the error:

protein = Protein('3eyg', ligand_ref='MI1')

Here is the corresponding ligand part in the pdb file:

Is that a wrong usage of ligand_ref parameter? I've noticed that in the example, a residual name was required, when I use protein = Protein('3eyg', ligand_ref='1') , the error was ValueError: Molecule ID not found: 1. I tried A1 and the same error occured.

What should be the correct representation for this ligand?

My current solution is extract the ligand from the cocrystal and save it as a sdf file, create a Ligand object and pass it to the Protein function.

Thanks!

[msuruzhon]

Hi,

The correct way is indeed to specify it as ligand_ref='A1' or ligand_ref='1'. However, there used to be a small bug regarding regex detection, which I fixed some updates ago. If you update your version of ProtoCaller, it should hopefully fix it, as your example seems to be working for me.

[kexul]

Hi, How can I install the latest version of protocaller which has the patch you mentioned? I've tried install it by mamba install -c conda-forge -c omnia -c michellab -c essexlab/label/dev protocaller and mamba install -c conda-forge -c omnia -c michellab -c essexlab protocaller, no upgrade happened.

My current version of protocaller is:

# Name                    Version                   Build  Channel
protocaller               1.1.2               40_gf92127e    essexlab

Should I clone the dev branch from github and install it manually?

[msuruzhon]

Since the packages differ only by build numbers, I would uninstall protocaller and clean the cache before installing it again. I think conda caches the build numbers, so it won't update it, even when it should.

[msuruzhon]

I have also now released version 1.2.0, which changes the pdb2pqr dependency, and uses the latest propka, so you might want to try it out. It will be easier to update with conda install -c conda-forge -c omnia -c michellab -c essexlab protocaller=1.2.0 as well.