Ah -- excellent! This will make it easier to count over all discrete
molecules and let me address them -- Many thanks again
-Tom
On Mon, Feb 22, 2010 at 1:58 PM, Robert Hanson <[email protected]> wrote:
> and there is also
>
> getproperty moleculeInfo
>
>
> On Mon, Feb 22, 2010 at 3:57 PM, Robert Hanson <[email protected]> wrote:
>
>> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Download Intel® Parallel Studio Eval
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>>>>> Jmol-users mailing list
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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
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
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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
>>
>
>
>
> --
> 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
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
------------------------------------------------------------------------------
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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