APPENDIX D – VEGA SELECTION 2.0
The VEGA ZZ selection file (.sel) is used to store bonds, angles, distances, torsions, angles between two planes and multiple atom selections in a file to save the time required to do multiple analysis operations in which same selections are repeated several times (see the trajectory Selection Tool).
File format description:
Each record in the .sel file is defined by a case-insensitive keyword preceded by # character. The first line must be the file identification header:
The #Selection keyword must be followed by file format version as argument and by selection records:
#<SELECTION_TYPE> <SELECTION_NAME> <ATOM_1> <ATOM_2> ... <ATOM_N>
The <SELECTION_TYPE> is the selection type and 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 for each 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 can be atom numbers or atom descriptors in standard VEGA format. For more information about atom selection rules, 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|
Starting from 2.0 specifications, you can store in the TORSION record the parameters for the conformational search such as the starting torsion value (<BASE>), the number of steps (<STEPS>) in which the search is completed if it is a systematic conformational search, the rotation window (<END/WINDOW>) for the random searches or the end of the rotation for the systematic search and a Boolean flag (<ENABLED>) to take in consideration the torsion during the conformational search (for more details, see the AMMP dialog window):
#TORSION <SELECTION_NAME> <BASE> <STEPS> <END/WINDOW> <ENABLED> <ATOM_1> <ATOM_2> <ATOM_3> <ATOM_4>
All these parameters (coloured in red) are optional.
This is quisqua.sel file that can be used with quisqua.dcd trajectory placed in the Examples/Molecules directory.
#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