calculate command
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calculate command
Leif Laaksonen CSC 2001
Timm Uhlmann 2003
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#
# calculate average structure from a trajectory
#
calc$ulate avst$ructure
#
# calculate backbone dihedral angles for a protein
#
bbdi$hedrals
#
# calculate the clustering for atoms Seg Res Atm through the frames
# in a trajectory
#
clus$ter Seg Res Atm
#
# delete all cluster data
#
-clu$ster
#
# (re)calculate the atom connectivity information for Seg Res Atm
#
conn$ectivity Seg Res Atm
#
# calculate hydrogen bonds
#
hbon$ds Seg Res Atm
hbon$ds Seg Res Atm Colour
hbon$ds Seg Res Atm {Fred Fgreen Fblue}
hbon$ds Seg Res Atm nohy$drogens
-hbo$nds
#
# calculate correlation array for distance/angle/torsion array(s)
# numbered Iserie1 and Iserie2
#
corr$elation dist$ance Iserie1 Iserie2
angl$e Iserie1 Iserie2
tors$ion Iserie1 Iserie2
#
# calculate geometrical center for atoms Seg Res Atm
#
geomc$enter Seg Res Atm
#
# calculate mass center for atoms Seg Res Atm
#
massc$enter Seg Res Atm
#
# calculate distance between Seg1 Res1 Atm1 Seg2 Res2 Atm2
#
dist$ance Seg1 Res1 Atm1 Seg2 Res2 Atm2
#
# calculate angle between Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3
#
angl$e Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3
#
# calculate torsion between Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 Seg4 Res4
#
tors$ion Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 Seg4 Res4 Atm4
#
# calculate mean square displacement for atoms Seg Res Atm using
# geometrical center
#
msdi$splacement atom Seg Res Atm
#
# calculate mean square displacement for atoms Seg Res ATm using
# mass center
#
msdi$splacement mass$center Seg Res Atm
#
# fit the atoms Seg1 Res1 Atm1 in system #1 to
# atoms Seg2 Res2 Atm2 in system #2
# 0 = numerical display off, 1 = numerical display on
#
quat$fit StrucN1 Seg1 Res1 Atm1 StrucN2 Seg2 Res2 Atm2
0/1
#
# calculate root mean square fluctuation for atoms Seg Res Atm
# through the frames
#
rmsf$luctuation Seg Res Atm
#
# calculate radial distribution function for atoms Seg2 Res2 Atm2
# calculated from Seg1 Res Atm1. The calculation will only
# be done for the current structure (system) displayed! However
# applying the command successively will add the new calculated
# rdf to the previous one(s) calculated. This enables the calculation
# of rdf for the full set of frames in a trajectory. To reset the
# calculation apply the "calc -rdf" command.
# To calculate the average from a set of applied "calc rdf" commands
# apply the "calc rdfmean" command.
#
rdf Seg1 Res1 Atm1 Seg2 Res2 Atm2 Fcut Tbin
-rdf
rdfm$mean
#
#
# calculate a plane from three points
#
plan$e fx1 fy1 fz1 fx2 fy2 fz2 fx3 fy3 fz3
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LUL/2001
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