Re: [Jmol-users] selecting a residue using only an atomno that is part of it

[Robert H. <ha...@st...>]

and there is also

getproperty moleculeInfo

On Mon, Feb 22, 2010 at 3:57 PM, Robert Hanson <ha...@st...> 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 <tho...@gm...>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 <ha...@st...>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 <
>>> rev...@us...> wrote:
>>>
>>>> Hallo Alexander,
>>>>
>>>> On Mon, Feb 22, 2010 at 14:40, Alexander Rose
>>>> <ale...@we...> 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&#174; 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
>>> Jmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; 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
>> Jmo...@li...
>> 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
>



-- 
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