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proto (c47b2)


Often a system contains many identical groups/molecules, which
during analysis should be treated uniformly; the most obvious example
being solvent waters. While several analysis routines do handle water
molecules separately, there are no provisions if another solvent is
used or if a mixture is studied. The PROTo facility provides a
framework for other CHARMM-modules (such as SHELL or RDFSOL) to treat
completely generic groups in a uniform, systematic manner. At the
moment a maximum of 10 prototype sets are supported simultaneously.

* Syntax | The syntax of the PROTo commands
* General | General overview
* Define | Defining a new Prototype
* Remove | Delete a prototype
* Image | Adding image prototypes to the list
* Info | Printing prototype information
* Caveats | Some limitations/todos to keep in mind
* Examples::

Syntax for the PROTo commands



PROTO [ DEFIne int ] [ atom-selection atom-selection ]
[ PNUM int atom-selection ]

[ REMOve int ]

[ IMAGe int ]

[ INFO ]

atom-selection::= see » select

General overview

The PROTO module allows the definition of a set of identical
subtypes in a selection (e.g. all methanol molecules in a
water/methanol mixture). These units can then be used in various other
which are specific to these entities.

PROTOtype definition

PROTO must be called once to set up a prototyped set of
entities before they can be used in other modules. Later this
prototype set can be referenced by the number given after the DEFINE
keyword. The command can be called in two ways:

Either two atom selections are given or a single atom selection along
with the number of atoms to bundle into a single entity is
used. Usually PROTO is called with two atom selections where the first
selection gives a single entity (the "prototype") while the second
selection lists all atoms from which these entities are to be
picked. This is done by using a "pivot atom" (usually the first atom
of the prototype selection) and saving the relative atom numbers of
the prototype atoms with respect to this pivot. In a second step then
all occurances of this pivot atom are picked from the second atom
selection are singled out and form the basis for the given prototype
set. This means that the second selection need not (but should) hold
the whole entities represented by this prototype set but only the
picked pivot atom (although this should not be relied upon since the
choice of the pivot atom may be changed in future versions).

In the second case only a single atom selection together with the
parameter PNUM is used. Here the first atom in the selection is used
as pivot atom and all similar atoms picked from the selection
list. The sets defined in this mode are the PNUM atoms following
consecutively in the atom number list after these pivot atoms.

Removing prototype sets

With the REMOve command the selected prototype set will be
deactivated and all associated memory will be cleared. After this
command the corresponding set will no longer be available to other


This command will simply add all images of the selected pivot
atoms to the selected prototype set. This procedure faces a simple
problem: at the outer border of the generated image atoms the sets may
be incomplete (i.e. some image atoms for a single entity may be
missing since they are too far away from the primary atom space). To
avoid having other modules use such incomplete sets (since they would
probably generate wrong data) the algorithm checks each of these
"image sets" for completeness. Thus some of the fringe image atoms may
not be included although they are images of selected primary pivot
atoms. This needs to be taken into account when CUTIM is specified in
the image setup (see » images ). For instance
if radial distribution functions for prototypes are to be calculated
using RDFSOL, CUTIM must not only be at least as large as the largest
distance the RDF is to be computed for, but has to be augmented such
that all sets at this distance are still complete if they are pointing
"outward" (this is of course dependent on the size of the prototype


The INFO command prints general informations about all
defined prototype sets. This comprises the relative atom numbers with
respect to the pivot atoms and the number of pivot atoms considered.

At print level 6 or higher the atom numbers for the selected
pivot atoms will also be printed.


- Only atoms similar to the pivot atom picked from the prototype
selection (or the first atom of the selection, if PNUM is used) will
be considered from the general atom selection. This mechanism should
not be relied upon to be robust but rather all sets to be considered
should be included in the second (or only) atom selection.

- When image sets are to be used (e.g. in RDFSOL) it must be
considered, that fringe sets will be disregarded if they are
incomplete (see Images for further detail).


!Puts all TIP3 waters into the first prototype.

! Suppose segment A contains all methanol molecules in a water/methanol
! mixture. then
!prototype set 2 contains all methanols present in the system