[PyMOL] centerofmass command gives error

2023-05-23 Thread Petro 
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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Re: [PyMOL] centerofmass command gives error

2023-05-23 Thread Jared Sampson 
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  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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Re: [PyMOL] centerofmass command gives error

2023-05-23 Thread Petro 
Thanks.
Yes it helps.


On Tue, 23 May 2023 at 15:21, Jared Sampson 
wrote:

> 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  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'
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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