Step 1: How to start the HKL-2000 program?

This section explains how to start the HKL-2000 program and set the working environment.

How do I start?

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

Then type

> HKL2000

Can I start from any directory?

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.

What are the files that make up the HKL-2000 suite, and what do they do?

• 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