Thanks for the info. I also didn't realize that states started at 1. Maybe the nonexistent state warning is something that should be implemented elsewhere as well.
As for the implicit *or*, you can find it in https://pymolwiki.org/index.php/Selection_Algebra#Selection_Operator/Modifier_Table under the *Logical* section. I agree that it can be easy to miss—good thing you caught this behavior in your code. Have a great day, Cole On Fri, Aug 9, 2019 at 6:34 PM Pedro Lacerda <pslace...@gmail.com> wrote: > 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 <pslace...@gmail.com> > escreveu: > >> Question answered. >> >> Best regards! >> >> Em sex, 9 de ago de 2019 às 12:33, Christian "Cole" French < >> christian.fre...@schrodinger.com> 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 <pslace...@gmail.com> >>> 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 <pslace...@gmail.com> >>>> 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* >>>> _______________________________________________ >>>> 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 >>> >>> >> >> -- >> Pedro Sousa Lacerda >> >> >> *Laboratório de Bioinformática e Modelagem Molecular* >> *Faculdade de Farmácia / UFBA* >> >> *@pslacerda* >> >> *+55 71 9 9981-1856* >> > _______________________________________________ > 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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