On Mon, Jul 18, 2011 at 10:17 AM, Dean Johnston <[email protected]>wrote:
> Bob,
>
> I had a question about that - does having a large number (i.e. thousands)
> of hidden atoms slow Jmol down at all relative to deleting unwanted atoms?
> In my case I knew that I wouldn't need to display some atoms, so I didn't
> care if they were deleted. But I didn't know if there was a benefit to
> deleting them. I agree that hiding them could let you switch between the
> different packing choices without having to re-load the cif.
>
Shouldn't have an effect. Deleted atoms are only removed if an entire model
is removed. Otherwise they are just permanently hidden.
Bob
>
> Dean
>
>
> On Mon, Jul 18, 2011 at 10:38 AM, Robert Hanson <[email protected]>wrote:
>
>> Thanks, Dean.
>>
>> Minor point: Generally I would recommend "display..." instead of "delete
>> not..." That gives you more flexibility.
>>
>> Bob
>>
>> On Sun, Jul 17, 2011 at 9:29 PM, Dean Johnston <[email protected]>wrote:
>>
>>> Simon,
>>>
>>> Here's what I've used. It obviously only works for molecular systems and
>>> can be somewhat slow for very large molecules/unit cells. Bob can probably
>>> figure out a more efficient way to do this, but it works for me. In these
>>> examples I've deleted any molecules that I don't want to see - you may want
>>> to just hide/display molecules instead.
>>>
>>> (1) I think this is equivalent to what Bob had suggested before - similar
>>> to Mercury's "include atoms in molecules where *Any* atom fits".
>>>
>>> load xxx.cif {333 777 1}; delete not within(molecule, unitcell);
>>>
>>>
>>> (2) Or (more complicated) - I think this is similar to Mercury's
>>> "include atoms in molecules whose *Centroids* fit".
>>>
>>> load xxx.cif {333 777 1};
>>> delete not within(molecule, unitcell);
>>> n = getProperty("moleculeInfo").size;
>>> for (var i=1; i<=n; i++)
>>> {
>>> select molecule=i;
>>> if (({selected}.fx < -0.001) || ({selected}.fx > 1.001) ||
>>> ({selected}.fy < -0.001) || ({selected}.fy > 1.001) || ({selected}.fz <
>>> -0.001) || ({selected}.fz > 1.001))
>>> { hide (hidden || {selected}); }
>>> };
>>> delete hidden;
>>>
>>> Dean
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> AppSumo Presents a FREE Video for the SourceForge Community by Eric
>> Ries, the creator of the Lean Startup Methodology on "Lean Startup
>> Secrets Revealed." This video shows you how to validate your ideas,
>> optimize your ideas and identify your business strategy.
>> http://p.sf.net/sfu/appsumosfdev2dev
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
AppSumo Presents a FREE Video for the SourceForge Community by Eric
Ries, the creator of the Lean Startup Methodology on "Lean Startup
Secrets Revealed." This video shows you how to validate your ideas,
optimize your ideas and identify your business strategy.
http://p.sf.net/sfu/appsumosfdev2dev
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