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# In this example, we create a coarse-grained representation of a dsDNA spherical spiral, such as we may find in a dsDNA virus.
# We will create a synthetic density map to represent this DNA. Then we will add noise and output the map.
firstStage 2
lastStage 2
# If we leave readPreviousFrameFile 1 (the default), then the ions at stage n will have the same coordinates as last.(n-1).pdb. So let's turn off structure file reading:
readPreviousFrameFile 0
# if we do stage 1, where readPreviousFrameFile is false, then monoAtoms will be adopted with an offset.
# We don't need the time integrator at all, in this case. We can't turn it off, so just numReportingIntervals to the minimum possible value:
numReportingIntervals 1
# We wil need the constant Pi, so define a user variable:
@pi 3.14159265358979
# We will create a single chain, chain ID Z:
spiralDNA chainID Z
# Spiral will be right handed:
spiralDNA spiralIsRightHanded 1
spiralDNA center 0. 0. 0.
spiralDNA radius 6.0
# The pitch turns out to be pretty constant, across shells:
spiralDNA pitch 2.3
# And of course this is also quite constant:
spiralDNA helixAdvancePerBasePair .34
# Leave out the north and south pole regions:
spiralDNA startTheta 0.5
spiralDNA endTheta 3.0
# This is a rotational offset, about the polar axis:
spiralDNA phiOffset 0*@pi/180
# We clear the frequencyPhaseAmplitudeVector, out of paranoia rather than necessity:
spiralDNA frequencyPhaseAmplitude clear
densityNoiseScale 1.0
densityNoiseTemperature 100.0
# This is where the fine grained structural coordinates will be written:
#spiralDNA spiralPdbFileName spiral.pdb
# This is the P68 density map, provided by Dominik Hrevik and Pavel Plevka:
#density densityFileName LocalRef_02_Cl02_res85_nocaps2_box.mrc
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