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:

#Selection 2.0

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
DISTANCE 2
ANGLE 3
TORSION 4
PLANEANGLE 6
MULTI No limits

 

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.

 

 

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