Str_check_add_hydrogens

BioBB
1

Hi all,

I’ve run into 2 issues related to the check_structure tool.

  1. keep_h, listed here is not actually supported with version biobb version 3.7.6 (my check_structure version is 3.9.11). I get this warning when I try to use it:
/home/pbarletta/anaconda3/envs/locuaz/lib/python3.7/site-packages/biobb_common/generic/biobb_object.py:71: UserWarning: Warning: keep_h is not a recognized property. The most similar property is: ph
  error_property, close_property))

And indeed, when I check the docstrings for StrCheckAddHydrogens, it’s not there.

  1. I can’t understand the selection syntax for the add_hydrogen command.
    Say I want to add hydrogens to the 3rd residue of the B chain, which is a glutamate.
    If I use this properties dictionary:
prop = {
    'charges': False,
    'mode': 'list',
    'list': "GLU3GLU"
}

I get an error:

h_rules[ion_res_list[res]] 
KeyError: False

And if I use this one:

prop = {
    'charges': False,
    'mode': 'list',
    'list': "GLU3GLU"
}

it runs, but it modifies every residue. I tried some other variations, sometimes I’d get this:

#ERROR: no mutations available for *:GLUB3

I couldn’t get it working on the terminal either (calling check_structure directly).

I’d appreciate any help on these issues.

Cheers,

2

Hi,

  1. keep_h will be added to the Building-block, thanks for pointing this out.
  2. add_hydrogen indeed adds hydrogen atons to all residues in the protein. This is the intended behaviour. It is not possible to add H only to some residues (the functionality could be added but I’m not sure in which scenario this this could be necessary).
    The provided selection option allows to define which protonation states shoud be used when they are not the default (GLU will become a negatively charged Glu by default, no need to indicate, to get a neutral one the selection would be GLU3GLH). In any case I will check the error that should not appear (as you are asking for the default protonation state).
    Hope this helps.

Josep L.

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