Re: [PyMOL] centerofmass command gives error

[Jared S. <jar...@co...>]

Hi Petro - It looks like that structure has a deuterium atom.  Assuming
you're interested in the non-deuterated molecule, you can convert it to a
hydrogen and the command will work.

```
alter elem D, elem="H"
rebuild
print(cmd.centerofmass("polymer"))
```

Or if you want to stick with Python API syntax, the first two commands
would be:

```
cmd.alter('elem D', 'elem="H"')  # note the second argument is a string for
the `expression` keyword arg, thus double quotes inside single quotes
cmd.rebuild()
```

Hope that helps.

Cheers,
Jared

On Tue, May 23, 2023 at 6:44 AM Petro <sub...@kh...> wrote:

>
> Hi everybody
> I get the following error when I try to use center of mass commanand.
> Any Idea what is wrong?
> Thanks.
> Petro.
>
> --------------------------------------------------------------------------KeyError                                  Traceback (most recent call last)
> Cell In[4], line 4      2 cmd.reinitialize()      3 cmd.fetch('1AKK')----> 4 cmd.centerofmass('polymer')
>
> File ~\miniconda3\envs\pymol\lib\site-packages\pymol\querying.py:1565, in centerofmass(selection, state, quiet, _self)   1563 model = _self.get_model(selection, state)   1564 for a in model.atom:-> 1565     m = a.get_mass() * (a.q or 1.0)   1566     com = cpv.add(com, cpv.scale(a.coord, m))   1567     totmass += m
>
> File ~\miniconda3\envs\pymol\lib\site-packages\chempy\__init__.py:82, in Atom.get_mass(self)     80 def get_mass(self):     81     '''Given the chemical symbol the atomic mass is returned'''---> 82     return atomic_mass[self.symbol]
> KeyError: 'D'
>
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