Chapter 1: Starting the Program and Setting the Data Sets
Step 1: How to start the HKL-2000 program?
This section explains how to start the HKL-2000 program and set the working environment.
Hopefully someone has set up an alias and you have a path so that you can just type HKL2000 or some equivalent. Otherwise, the program is usually installed in /usr/local/bin and can be started by typing /usr/local/bin/HKL2000. Alternatively, the program can be installed in any directory. In that case the user has to set environmental variable HKLPATH to that directory. For instance if all programs are installed in the directory /home/user/prog2000, it is necessary to execute commands:
> setenv HKLPATH /home/user/prog2000
> alias HKL2000 $HKLPATH/HKL2000
No. You must have file writing permission in your working directory, because the program writes the files reject, peaks.file, hklpredictions, den.in, den.out, scl.in, xdisp.in, and xdisp.out, to the working directory. What are these files?
reject is the list of rejected reflections created in scaling
peaks.file is the file that contains peaks selected by PeakSearch routine
hklpredictions is a binary file that contains a listing of predicted reflection positions
den.in is a listing of the commands used to run the indexing
den.out is a modified log file of the indexing
scl.in is the Scalepack input file
xdisp.in and xdisp.out are input and output files for the display program.
HKL2000 – Main program package with the Graphical User Interface
access_prod - Program that prepares file necessary for license key generation. It has to be executed on each computer that will run HKL-2000 suite.
anomalous - Anomalous signal analysis
cdir_t - Directory manipulation tools
denzo_3d – Auto-indexing, refinement and integration; 3-D processing
hklfilename - File name manipulation tools
hklsysinfo - Program that gathers information about computer resources
readheader - File header reader
scalepack - Data scaling for 2000 frames and 2 million reflections
scalepack16m - Data scaling for 2000 frames and 16 million reflections
scalepack8m – Data scaling for 2000 frames and 8 million reflections
scalepackmanyframes - Data scaling for 4000 frames and 2 million reflection
scalepackvirus – Data scaling for 2000 frames and 32 million reflections
strat – Strategy and simulation
suser - internal communication program
xdark - dark current calculation
xdisp - Image display and measurement
Table of Contents
Detector and Site Info