fixed -- only a problem in the 13.1.9_dev.
releasing 13.1.9.
On Thu, Nov 22, 2012 at 9:16 AM, Simone Sturniolo <simonesturni...@gmail.com
> wrote:
> 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 <angel.herr...@uah.es>
>
>> 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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>
>
>
> --
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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