Re: [PyMOL] count_atoms and states

[Pedro L. <psl...@gm...>]

So missing boolean operators are filled with OR, for me this is should be a
big and loud WARNING. I almost messed everything up because it almost
passed in my tests.

Also I mistake states a couple of days on multi-model files because I was
counting from ZERO but states starts on ONE. That was until I needed
get_area, it properly stated that my states were nonexistant.

So these were my personal thoughts and issues about.

Have a nice weekend!

Em sex, 9 de ago de 2019 12:41, Pedro Lacerda <psl...@gm...>
escreveu:

> Question answered.
>
> Best regards!
>
> Em sex, 9 de ago de 2019 às 12:33, Christian "Cole" French <
> chr...@sc...> escreveu:
>
>> Hi Pedro,
>>
>> *count_states* is correct here; there's only 1 state, which is state 1.
>> The reason for the observed *count_atoms* behavior is that "polymer" and
>> "state" are different operators in the selection algebra, so putting them
>> together without a logical operator such as "and" or "or" between them
>> indicates an implicit "or". So you're actually counting atoms which match
>> "polymer" *or* "state X", which is why the number only goes up to 8627
>> when you count state 1.
>>
>> This might clear up your scope question as well, but please indicate if
>> otherwise.
>>
>> Best,
>> Cole
>>
>> On Fri, Aug 9, 2019 at 10:55 AM Pedro Lacerda <psl...@gm...>
>> wrote:
>>
>>> I'm also puzzled by the scope of state:
>>>
>>> *PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>>>>  count_atoms: 8205 atoms
>>>>
>>>> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>>>>  count_atoms: 8109 atoms
>>>>
>>>> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>>>>  count_atoms: 8109 atoms
>>>>
>>>> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>>>>  count_atoms: 192 atoms
>>>>
>>>> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>>>>  count_atoms: 0 atoms
>>>>
>>>
>>> Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
>>> escreveu:
>>>
>>>> Hi,
>>>>
>>>> There is only one state but the atom counting changes between states 0,
>>>> 1 and 2.
>>>>
>>>>
>>>> What this means?
>>>>
>>>> *PyMOL>fetch 1e92*
>>>>>
>>>>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>>>>  ExecutiveLoad-Detail: Detected mmCIF
>>>>>  CmdLoad: loaded as "1e92".
>>>>>
>>>>> *PyMOL>count_atoms polymer state 0*
>>>>>  count_atoms: 7917 atoms
>>>>>
>>>>> *PyMOL>count_atoms polymer state 1*
>>>>>  count_atoms: 8627 atoms
>>>>>
>>>> *PyMOL>count_atoms polymer state 2*
>>>>>  count_atoms: 7917 atoms
>>>>>
>>>> *PyMOL>count_states *
>>>>>  cmd.count_states: 1 states.
>>>>>
>>>>
>>>> --
>>>> Pedro Sousa Lacerda
>>>>
>>>>
>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>> *Faculdade de Farmácia / UFBA*
>>>>
>>>> *@pslacerda*
>>>>
>>>> *+55 71 9 9981-1856*
>>>>
>>>
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>> _______________________________________________
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>>
>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>