Re: [Jmol-users] Application oddities - V13.1.9_dev

[Simone S. <sim...@gm...>]

Oh, good to know. Currently I am working on 13.1.9_dev, so it's a new bug.
I am interested into using this notation because it's very regular and
seems more practical for scripting than, say, using the full chemical name.

By the way, hello everyone. I'm a new one but I'm going to hang around on
this list quite a lot, since my new job involves writing a JMol based
webpage.


2012/11/22 Angel Herráez <ang...@ua...>

> Ciao Simone
>
> > I support this idea. Also, I remember reading somewhere that
> > selectionHalos is supposed to be set ON by default when a file is
> > loaded - which in my case actually does not happen when I load from
> > the scripting console.
>
> I don't think so. In my experience this has never been so, and it is
> a bad idea since upon loading ALL atoms are selected by default.
>
>
> > This works for me, however, only when I refer to those atoms by
> > using their 'label' names (e.g. O3, H1, C7 etc).
>
> In formats like mol this works. For pdb format, you need the bio
> specification, like *.OB or *.CA or 26SER.CA.
>
>
> > 'species array' notation - e.g. (_O)[1], (_Si)[4] - it is not
> > possible for me to select multiple atoms in this way
>
> I did not know about this notation, but I just tested and it works,
> at least  in 13.0.8:
>
> $ load $caffeine
> $ select (_O)[1]
> 1 atoms selected
> $ select (_O)[1] or (_N)[2]
> 2 atoms selected
> $ select (_O)[1], (_N)[2]
> 2 atoms selected
>
> Ah, it's broken in 13.1.8
>
>
>
>
>
>
>
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