APPENDIX D –  VEGA SELECTION 1.0

The VEGA selection file (.sel) is used to store pre-defined distances, angles, torsions, angles between two planes and multiple atom selections in a file in order to reduce the time during multiple analysis operations (see the trajectory Selection Tool).

File format description:
Each record in the .sel file is defined by a keyword with the # at the beginning, written in upper or lower case. The first line must be the file identification header:

#Selection 1.0

The #Selection keyword must have the file format version as argument and can be followed by one or more record defining a selection:

#<SELECTION_TYPE> <SELECTION_NAME>
<ATOM_1>
<ATOM_2>
...
<ATOM_N>

The <SELECTION_TYPE> is the type of the selection and it can be: DISTANCE, ANGLE, TORSION, PLANEANGLE and MULTI. The <SELECTION_NAME> is the user-defined name of the selection. This must be an unique name in the selection type (e.g. two angles named Ang_1 can't exist, but one angle and one torsion with the same name are allowed). The <ATOM_1> to <ATOM_N> tags are the atom description in the standard VEGA format or the atom number. For more information about the VEGA atom selection conventions, click here. The number of the <ATOM_N> lines is defined by the selection type, as shown in the following table:

Selection Type Number of ATOM lines
DISTANCE 2
ANGLE 3
TORSION 4
PLANEANGLE 6
MULTI No limits

 

Example:
This is the quisqua.sel file that can be used with quisqua.dcd trajectory placed in the Molecules directory.

#Selection 1.0
#DISTANCE "Dist_1"
N10:QUIS:1:*:1
O16:QUIS:1:*:1
#ANGLE "Ang_1"
C11:QUIS:1:*:1
C7:QUIS:1:*:1
C6:QUIS:1:*:1
#TORSION "Tor_1"
C7:QUIS:1:*:1
C6:QUIS:1:*:1
N3:QUIS:1:*:1
O2:QUIS:1:*:1