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How is atom-spec different from atom selection?
#32374 08/09/13 03:13 PM
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My forum search found no explanation.
Thankyou people/

Re: How is atom-spec different from atom selection?
swmmr1928 #32375 08/09/13 03:54 PM
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From the ENTER syntax listing in correl.doc--

Code:
      atom-spec::= {residue-number atom-name}
                   { segid  resid atom-name }
                   { BYNUm  atom-number     }
                   { SELE atom-selection END} ***
 
      atom-selection::= see *note Selection:(select.doc)
      *** Note: If an atom-selection is used for atom-spec's, then
          all atom-spec's must be contained within one atom-selection


Some parts of CHARMM allow the atom-spec, esp. in cases where the ordering of atoms is significant, such as commands involving angles or dihedrals, identifying vectors, and IC SEED. An issue is that atom selection always returns the atom list in PSF order, which may not be what is intended.

In this case an atom selection is one of the allowed options, but should probably not be used for ANGL or DIHE time series.


Rick Venable
computational chemist

Re: How is atom-spec different from atom selection?
swmmr1928 #32376 08/09/13 04:17 PM
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Alright.

I want to focus on enter dist because I want the distance between one atom and the center of mass of a micelle.
Center of mass can be found from coor stat, but how is this incorporated into the enter dist command?

I do not understand the note about using atom select.
Code:
*** Note: If an atom-selection is used for atom-spec's, then
          all atom-spec's must be contained within one atom-selection


You previously gave this example:

Code:
enter d0 distance select type C1Q .or. type C4Q end 


Is ".or." the only way to separate the two selected atoms (comply with the note)?

Last edited by swmmr1928; 08/09/13 04:38 PM.
Re: How is atom-spec different from atom selection?
swmmr1928 #32377 08/09/13 04:46 PM
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To best identify single atoms, my preference is to always use the ordered triplet SEGID RESID TYPE atom-spec, e.g.

enter d0 distance L 1 C1Q L 1 C4Q

While the .OR. atom selection may work, it is ambiguous in the case where more than a single molecule has the named atoms (C1Q, C4Q). The atom-spec is both more concise and explicit, and usually the best choice for single atoms.


Rick Venable
computational chemist

Re: How is atom-spec different from atom selection?
swmmr1928 #32378 08/09/13 04:54 PM
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I'll start a new topic for my specific question.


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