this is fixed.
On Mon, May 5, 2014 at 5:13 PM, Robert Hanson <[email protected]> wrote:
> Beware of using atomIndex and atom/model deletion.
>
> When deleting atoms, atomIndex is not changed. There are just some missing.
> When a model is deleted, whole sections of the model atom array are
> excised, and all objects referring to atoms by atom number are recreated.
>
> However, there is a bug. Using zap {1.1} after deleting atoms in model 2.1
> results in those deleted atoms in magically reappearing but not behaving
> properly.
>
> Bob
>
>
>
>
>
> On Mon, May 5, 2014 at 9:44 AM, Otis Rothenberger
> <[email protected]>wrote:
>
>> Bob,
>>
>> In a sequence of model editing operations involving the following, I end
>> up with some atomno/atom-index confusion. The editing steps are:
>>
>> 1) Model bond change.
>> 2) Model duplication.
>> 3) Single model delete.
>>
>> After this sequence, atomno seems to lose its mathematical relationship
>> to atom index. This is based on the observation that using bond pick
>> callback atomno to calculate atom index leads to branch selection problems.
>> That the relationship between atomno and atom index is the problem is
>> verified by the following:
>>
>> select atomno=18;prompt({selected}.atomIndex) -- where 18 represents
>> any atomno being tested.
>>
>> Prior to the editing, the above produces the expected atomno-1. After the
>> above editing, the above produces atomno+1.
>>
>> This is not a problem with simple single model editing. The above
>> convolution of steps seems to create the issue.
>>
>> Is this a bug or just the consequence of convolution? Perhaps I should
>> just use atomno for my subsequent operations.
>>
>> Otis
>>
>>
>>
>> --
>> Otis Rothenberger
>> [email protected]
>> http://chemagic.com
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> 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
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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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