From 7eef35e69a80d078c134fc2b52a2bd71e9ee7091 Mon Sep 17 00:00:00 2001 From: jdickerson95 <32930629+jdickerson95@users.noreply.github.com> Date: Fri, 30 Nov 2018 10:47:19 +0000 Subject: [PATCH] switching --- .pydevproject | 5 ++ MicroEDInput.txt | 118 +++++++++++++++++++++++++++++++++++++++++++ output-DoseState.R | 0 output-DoseState.csv | 0 output-RDE.csv | 0 output-Summary.csv | 0 output-Summary.txt | 0 7 files changed, 123 insertions(+) create mode 100644 .pydevproject create mode 100644 MicroEDInput.txt create mode 100644 output-DoseState.R create mode 100644 output-DoseState.csv create mode 100644 output-RDE.csv create mode 100644 output-Summary.csv create mode 100644 output-Summary.txt diff --git a/.pydevproject b/.pydevproject new file mode 100644 index 00000000..d001f0ae --- /dev/null +++ b/.pydevproject @@ -0,0 +1,5 @@ + + +Default +python interpreter + diff --git a/MicroEDInput.txt b/MicroEDInput.txt new file mode 100644 index 00000000..b4641e24 --- /dev/null +++ b/MicroEDInput.txt @@ -0,0 +1,118 @@ +############################################################################## +# Crystal Block # +############################################################################## + + +Crystal + +Type Cylinder + + # Crystal shape can be Cuboid or Spherical + +Dimensions 0.8 2 + # Dimensions of the crystal in X,Y,Z in µm. + # Z is the beam axis, Y the rotation axis and + # X completes the right handed set + # (vertical if starting face-on). + +PixelsPerMicron 10 + # This defines the coarseness of the simulation + # (i.e. how many voxels the crystal is divided into.) + # Preferably set as high as possible, however for a higher + # value the simulation will take longer to complete. + # Recommended to try increasing between 0.5 and 5 and ensure + # the reported dose value converges as PixelsPerMicron increases. + # As a rule of thumb, this needs to be at least 10x the beam + # FWHM for a Gaussian beam. + # e.g. 20µm FWHM beam -> 2µm voxels -> 0.5 voxels/µm + +# NOTE: Use AngleP/AngleL if your crystal is not face-on to the beam. +# See RD3D user guide for more details + +# Also need to specify the crystal composition below (Example case for insulin given): +AbsCoefCalc RD3D + # Absorption Coefficients calculated + # using RADDOSE-3D (Zeldin et al. 2013). + +# PDB 2vb1.pdb + +UnitCell 78.02 78.02 78.02 + # unit cell size: a, b, c with alpha, beta and gamma angles default to 90° + +NumMonomers 24 + # number of monomers in unit cell + +NumResidues 51 + # number of residues per monomer + +ProteinHeavyAtoms Zn 0.333 S 6 + # heavy atoms added to protein part of the + # monomer, i.e. S, coordinated metals, Se in Se-Met + +SolventHeavyConc Na 1540 Cl 1540 + # concentration of elements in the solvent + # in mmol/l. Oxygen and lighter elements + # should not be specified + +SolventFraction 0.67 + # fraction of the unit cell occupied by solvent + +ANGLEL 90 + +#ELECTRONS TRUE +#SIMELECTRONS 100000 + +CALCULATEFLESCAPE FALSE +CALCULATEPEESCAPE FALSE +CALCSURROUNDING FALSE +#OILBASED TRUE +#OILELEMENTS Ag 1 +#OILDENSITY 19 + +#CONTAINERMATERIALTYPE ELEMENTAL +#MATERIALELEMENTS Si 1 +#CONTAINERTHICKNESS 300 +#CONTAINERDENSITY 2.3290 +############################################################################## +# Beam Block # +############################################################################## + +Beam + +Type TopHat + # beam profile can be Gaussian or TopHat +Flux 1e12 + # in photons per second (2e12 = 2 * 10^12) +# FWHM 1 1 + # in µm, horizontal by vertical for a Gaussian beam +Energy 300 + # photon energy in keV + +Collimation Rectangular 2 2 + # Horizontal/Vertical collimation of the beam + # For 'uncollimated' Gaussians, 3xFWHM recommended + +#Exposure 10 # in e-/A^2 + +#IMAGEDIM 0.2 0.2 + +#SEMIANGLE 0.00001 +#APERTURERADIUS 1.00001 + +############################################################################## +# Wedge Block # +############################################################################## + +Wedge 0 0 + # Start and End rotational angle of the crystal with Start < End + +ExposureTime 50 + # Total time for entire angular range + +# AngularResolution 2 + # Only change from the defaults when using very + # small wedges, e.g 5°. + +# NOTE: To define more complex geometries (helical, de-centred, or offset), +# see the StartOffset, TranslatePerDegree, and RotAxBeamOffset keywords +# in the User Guide \ No newline at end of file diff --git a/output-DoseState.R b/output-DoseState.R new file mode 100644 index 00000000..e69de29b diff --git a/output-DoseState.csv b/output-DoseState.csv new file mode 100644 index 00000000..e69de29b diff --git a/output-RDE.csv b/output-RDE.csv new file mode 100644 index 00000000..e69de29b diff --git a/output-Summary.csv b/output-Summary.csv new file mode 100644 index 00000000..e69de29b diff --git a/output-Summary.txt b/output-Summary.txt new file mode 100644 index 00000000..e69de29b