A python package that simulates powder diffraction using CCP4 and xprepx.
The powder script glues together operations to simulate powder diffraction using xprepx and ccp4.
The powder script installs to the bin/ directory of your Python install, which should be in your path.
Before running powder, make sure that the following programs and packages are available and in your path:
You also need Python version 2.6 or 2.7.
Running powder requires only four easy steps.
Make a new directory and put your pdb file in it.
Make a template settings file in that directory:
powder -t > settings.cfg
Edit at least the first five values in the settings file on the right hand side of the “=” signs.
Important - Don’t change the names on othe left of the “=” signs because the left hand side names have meaning.
Run powder with the config file you edited:
powder settings.cfg
Run powder with no arguments for quick help:
powder
The powder diffraction and a postscript file will be made for you. The program that does the summation and averaging, xprepx, runs as an X-window. When the plot pops up, it is important to click in the plot window and hit <Enter> to make sure the postscript file is saved.
A pdf file is now also made that summarizes the model and simulation. That file is named the same as the postscript output, except that the filename extension is ”.pdf”, of course. Contents of the file specified by the info setting will be inserted into this report.
There is no need to edit the pdb file in most cases. The CRYST1 card, which specifies the crystallographic symmetry, is created for you from the settings file and written to a new pdb file which is then used for the diffraction simulation.
An exception to modifying pdb files is that NMR structures should be limited to one model only. NMR structures come from the PDB with more than one model included. The extra structures will influence the powder diffraction.
A text file will now be created that contains YAML (http://en.wikipedia.org/wiki/YAML) describing the spectrum as taken from the xprepx postscript output. The name of this file is specified by the spectrum file setting (default: spectrum.yml). In YAML terms, the spectrum is stored as a top-level list of [2-theta, intensity] pairs. A python program can make a 2-D numpy array from the spectrum easily if numpy (http://numpy.scipy.org/) and pyYAML (http://pyyaml.org/) are installed. For example, if the spectrum is stored in the file “spectrum.yml”:
import numpy
import yaml
spec_ary = numpy.array(yaml.load(open('spectrum.yml')))
More generally, the spectrum starts on the second line of the yaml file and each data line conforms to the following FORTRAN formatted read:
REAL X, Y
READ '(4X, F9.0, 2X, F9.0)', X, Y
The -d flag prevents powder from running xprepx and CCP4 programs for debugging.
The -t flag will print a template file for editing (see the instructions).
The -c flag with the config file will give a 2-theta -> resolution conversion for the wavelength specified in the config file. E.g.:
powder -c settings.cfg
The -h flag will print the usage and help notes.
The settings file is a standard sectionless config file in the standard INI file format (http://en.wikipedia.org/wiki/INI_file).
Examples of minimimal and complete settings files are at the end of this manual.
The “powder” script will fail if these minimal settings are not included in the settings file.
pdb model: the name of the pdb file containing the model (e.g. my_model.pdb) cell dimensions: three numbers separated by spaces that specify the dimensions of the unit cell (e.g. 250 250 250) res limits: two numbers separated by spaces that specify the low and high resolution limits over which to calculate the simulated powder diffraction spectrum (e.g. 1000 4.0) wavelength: the wavelength of the simulated x-ray radiation (e.g. 1.54178) postscript file: name of the output postscript file that shows the simulated spectrum (e.g. my_powder.ps)
These settings are not necessary but are included for special cases, like using non-standard versions of sfall, xprep, etc.
reset b-facs: a number that specifies a new b factor for all atoms in the model–if this number is negative, then no reset will be done (default: -1) mark interval: for the plotted spectrum, the interval between marks on the 2-theta axis (default: 2) title: for the pdf report, the title will pe placed in the report above the simulated diffraction pattern (default: info.txt) info: name of info file that contains pre-formatted text that will be inserted into the pdf report (default: info.txt) clean up: if set to True, then the mtz & sca files will be removed to save disk space (default: True) plot x units: if set to angstroms, then theta angles along the x-axis are converted to angstroms instead of the xprepx default of degrees (default: angstroms) side ps file: name of an intermediate ps file showing a side view of the model–use it if you don’t want a hidden file (default: .tmp.side.ps) top ps file: name of an intermediate ps file showing a top view of the model–use it if you don’t want a hidden file (default: .tmp.top.ps) spectrum file: name of the yaml file in which the spectrum will be stored as a numerical 2-d array (default: spectrum.yml) temp pdb file: powder must create an intermediate pdb file (default: .tmp.pdb) mtz file: powder must create an intermediate mtz file (default: my_model.mtz) sca file: powder must also create an intermediate sca file that will also serve as the root name for the xprep prp results file (default: my_model.sca) sfall: command to call the sfall program from CCP4 (default: sfall) mtz2various: command to call the mtz2various program from CCP4 (default: mtz2various) xprepx: command to call xprepx–if you have memory problems, use bigxprepx, i.e. /joule2/programs/xprep/bigxprepx (default: xprepx) ps2pdf: command to convert postscript to pdf (default: ps2pdf) molauto: command to call molauto for making views of model (default: molauto) molscript: command to call molscript to make views of model (default: molscript) convert: command to convert different image formats (default: convert)
# minimal settings file for powder
pdb model = my_model.pdb
cell dimensions = 200 200 200
res limits = 1000 4.0
wavelength = 1.54178
postscript file = my_powder.ps
# complete settings file for powder
pdb model = my_model.pdb
cell dimensions = 200 200 200
res limits = 1000 4.0
wavelength = 1.54178
postscript file = my_powder.ps
# New B factor (-1 for no reset)
reset b-facs = -1
# 2-Theta Interval Marks
mark interval = 2
# Title of simulation
title = My Model
# Name of file that contains info about model
info = info.txt
# Clean up sca and mtz files
clean up = True
# Units of x axis for plot
plot x units = angstroms
# Name of intermediate ps file for side view
side ps file = side.ps
# Name of intermediate ps file for top view
top ps file = top.ps
# Name of file to store spectrum as yaml
spectrum file = spectrum.yml
# Name of intermediate pdb file
temp pdb file = powder-tmp.pdb
# Output mtz File
mtz file = my_model.mtz
# Output Scalepack File
sca file = my_model.sca
# Command to call sfall
sfall = sfall
# Command to call mtz2various
mtz2various = mtz2various
# Command to call xprepx
xprepx = xprepx
# Command to call ps2pdf
ps2pdf = ps2pdf
# Command to call molauto
molauto = molauto
# Command to call molscript
molscript = molscript
# Command to convert image formats
convert = convert