Right. The groupID of non-PDB atoms is 0.
But Jmol will construct the molecules.
print {atomno = 3}.molecule
for instance. These two are synonymous:
x = {atomno=3}.molecule
select molecule = x
and
select within(molecule, atomno=3)
On Mon, Feb 22, 2010 at 3:43 PM, Thomas Stout <[email protected]>wrote:
>
> And just to clarify my understanding: there is no concept of "GROUP" for
> non-PDB/mmCIF files, correct?
>
> I am currently battling a similar logic problem & I think what I need to do
> is write my own group(index) variable to count up the number of discrete
> molecules in a coordinate file. So, for example, I would clump together the
> first loaded atom & all atoms to which it was covalently bonded, then take
> the next atom that is not in the first clump & all its bonded mates, et
> cetera.
>
> -Tom
>
>
>
>
> On Mon, Feb 22, 2010 at 1:36 PM, Robert Hanson <[email protected]> wrote:
>
>> Careful -- "3" there is what we call the "atomIndex" not the "atomNumber"
>> -- the distinction there is that "atomIndex" starts at 0, and atomNumber
>> could be anything depending upon the file, but usually starts with 1. Better
>> is:
>>
>> select atomno=3
>>
>> or
>>
>> select atomIndex=3
>>
>> just so you are more explicit about what you are selecting.
>>
>>
>>
>>
>> On Mon, Feb 22, 2010 at 3:10 PM, Oliver Stueker <
>> [email protected]> wrote:
>>
>>> Hallo Alexander,
>>>
>>> On Mon, Feb 22, 2010 at 14:40, Alexander Rose
>>> <[email protected]> wrote:
>>> > Hi all,
>>> >
>>> > maybe someone can help.
>>> >
>>> > I have an atomno, that I can select with 'select ({3})'. Now but I want
>>> to select the residue the atom is belongs to. Is that even possible?
>>>
>>> select within(GROUP, ({3}) )
>>>
>>> > Thanks.
>>> >
>>> > Greetings
>>> > Alex
>>> >
>>>
>>>
>>> Oliver
>>>
>>>
>>> ------------------------------------------------------------------------------
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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
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
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>>
>>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
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> 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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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