Software Download Instructions
HKL instructions

HKL-2000 instructions


HKL instructions

Executables of all programs can be obtained from our server hkl.hkl-xray.com. To download the programs, type the following instructions:

ftp hkl.hkl-xray.com

login: hklftp

password: The password can be obtained through the automatic password system (established users only) or by contacting us via e-mail.

If you have successfully connected to our server you may type:

ftp> ls

and you'll find directory ver1.98.2 with the following sub-directories:

Linux : HKL_Linux_ver_1.98.2.tar.Z and individual_programs (not tarred and not compressed)

SGI : HKL_SGI_ver_1.98.2.tar.Z  and individ_programs

*OSF_DigitalUnix : Due to extinction of this OS, the further support will be phased out. The last available version of HKL for OSF is 1.97.9

Each xxx.tar.Z file contains compressed and 'tarred' executables for corresponding operating system, while 'individual_programs' directory contains individual executables - not tarred and not compressed.

Remember, you have to use binary mode to transfer these files.

After you've transferred files, you have to uncompress them using the command:

uncompress file-name.tar.Z

for example:

uncompress HKL_Linux_ver_1.98.2.tar.Z

and 'untar' the file using the command:

tar -xvf file-name.tar

for example:

tar -xvf  HKL_Linux_ver_1.98.2.tar

You should have all the programs' executables now. 

access_prod
denzo
denzobig
scalepack
scalepack16m
scalepack8m
scalepacklvirus
scalepackmanyframes
scalepackmf6500
scalepacknorm
scalepackribo
scalepackvirus
xdisp

Typically the executables are placed in the

/usr/local/bin

directory. You need system privileges to do so. Additionally the license key file, cr_info, needs to be present in the

/usr/local/lib

directory in order for the HKL programs to run. To obtain the license key, you need to run the access_prod program on each computer that you plan to use for running any of the HKL programs. The access_prod is distributed together with denzo, scalepack, and xdisp executables.

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HKL-2000 instructions
Current Versions:
LinuxHKL2000_linux_ver_0.98.698o
SGIHKL2000_sgi_ver_0.98.695b
MAC OS X (Intel) HKL2000_MacIntel_0.98.698s
MAC OS X (Power PC)HKL2000_MAC_692i
OSFHKL2000_osf_ver_0.97.647d

You may download the HKL-2000 program executables from our server hkl.hkl-xray.com.

ftp hkl.hkl-xray.com

login: hkl2000ftp

password:

The password can be obtained through the automatic password system (established users only) or by contacting us via e-mail.

Please note that the HKL-2000 executables are in hkl2000ftp, not in hklftp.

If you have successfully connected to our server you may type:

ftp> ls

In ver_098.### directory there is a file anom.dat and the following sub-directories:

Linux :
> HKL2000_Linux_ver_0.98.###.tar.Z
> individual_programs (not tarred and not compressed)

MAC-INTEL:
> HKL2000_Macintel.###.tar.Z
> individ_programs

SGI:
> HKL2000_SGI_ver_0.98.###.tar.Z
> individ_programs

Each xxx.tar.Z file contains compressed and "tarred" executables for the corresponding operating system, while individual_programs directory contains individual executables - not tarred and not compressed. Remember that you have to use binary mode to transfer these files.

After you've transferred the files, you have to uncompress them using the command:

> uncompress file-name.tar.Z

for example:

> uncompress HKL2000_Linux_ver_0.98.###.tar.Z

and 'untar' the file using the command:

> tar -xvf file-name.tar

for example:

> tar -xvf  HKL2000_Linux_ver_0.98.###.tar

You should have all the programs' executables now. 

access_prod
anomalous
cdir_t
denzo
denzo_3d
HKL2000
hklfilename
hklsysinfo
readheader
scalepack
scalepack16m
scalepack8m
scalepacklvirus
scalepackmanyframes
scalepackmf6500
scalepackribo
scalepacktest
scalepackvirus
strat
suser
xdark
xdisp

Typically the executables are placed in the directory:

/usr/local/bin

You can also place the executables in an arbitrary directory, for instance

/home/joed/programs/hkl

In that case, you have to set the environmental variable HKLPATH to that directory. The exact command will depend on the shell you are using to run the programs. For tcsell and the above example, the command is:

setenv HKLPATH /home/joed/programs/hkl

There also should be created a directory:

/usr/local/hklint

You need system privileges to do it. The anom.dat file should be placed in this directory together with subdirectories containing the site files. The site file (def.site) of each detector (home or synchrotron) should be stored in its own directory. Each such directory should be appropriately named to easily identify the specific facility and the detector.

Example:

/usr/local/hklint/Raxis4
/usr/local/hklint/SPring8-BL23-Quantum4
/usr/local/hklint/BNLX25-Quantum4

Similarly, you can place the site files in arbitrary directory but as before, you have to set the environmental variable HKLDIR to the directory that contains anom.dat and subdirectories with the site files.

Additionally the license key file, cr_info, needs to be present in the /usr/local/lib directory in order for the HKL-2000 programs to run. One cr_info file may contain information about many computers and detectors. The program looks through the cr_info file for the right combination of fields that matches the given detector family and computer information. Other fields are ignored.

To obtain the license key, you need to run the access_prod program on each machine that you plan to use for running any of the HKL-2000 programs. Executing the access_prod results in the following dialog (answers in red):

  • enter the name of your institution: State University
  • enter the name of PI: John Doe
  • enter the name of person responsible for HKL maintenance: Jane Doe
  • enter names of all frame formats (detectors) you want to use: mar raxis4
  • enter the number of detectors in your lab which are currently supported by HKL package: 2
  • enter the name of company from which you received your license: HKL Research, Inc.
  • enter HKL version number: 0.98.689
  • if this is temporary license, enter the number of days you request, for permanent license enter 'noexpir': noexpir
  • do you want to send automatically e-mail to hkl@hkl-xray.com in order to activate your license (y) ? n

    If the answer is y (yes), the access_prod program may automatically send an e-mail with a request for an access file: cr_info. It not always works, though. If the answer is n (no) the program will produce the following info file. You may save the info file and afterwards 'manually' send it to hkl@hkl-xray.com.

Please:

  • Do not edit or alter the info file - it is processed automatically after verification.
  • Do not send an info file as an attachment.
  • Note that the access_prod program does not work properly if the set-up of the computer operating system is not consistent.

The example of an info file created by the access_prod program is given below (comments in italic):
HOST-NAME: p4.med.state.edu(extracted by the program - do not edit!)
NOTE: the field is limited in length to 30 characters
HOST-ID: -2035379618(extracted by the program - do not edit!)
HOSTNAM: state.edu(extracted by the program - do not edit!)
HW_PROV: sgi(extracted by the program - do not edit!)
CPU-SERIAL: sgi,CPU,1762854231(extracted by the program - do not edit!)
INSTITUTION: State UniversityLicensee's Institution name
PI: John DoePrincipal Investigator or Group Leader
CONTACT: Jane DoeContact Person
DETECTORS: mar raxis4Detector Format Families
NO-OF-DET: 2Number of Detectors at Home Laboratory
PROVIDER: HKLLicense Provider: Rigaku Americas Corporation, HKL Research, etc
VERSION: 0.98.689Requested Version of the Program
EXPIR: noexpir

The following are detector families to be used in the above "questionnaire":

  • dip - DIP family of scanners
  • raxis2 - RAXIS-II
  • raxis4 - RAXIS-IV
  • raxis5 - RAXIS-V
  • mar - MAR imaging plate detectors (except MAR345)
  • mar345 - MAR345 detector
  • brandeis - Brandeis 1k CCD detector on line X12c at BNL
  • unsup - ADSC Quantum-4 CCD detector
  • unsup210 - ADSC Quantum-210 detector
  • unsup315 - ADSC Quantum-315 detector
  • un-mar - MAR CCD detector 130mm
  • un-mar165 - MAR CCD detector 165mm
  • un-brand - CCD Brandeis 2x2

When you have the access file, cr_info, in /usr/local/lib directory, you should be able to run the program by typing:

HKL2000

Note 1: Access File
To obtain the access file, cr_info, please see Access Key for details.

Note 2: Site files for synchrotron detectors
Site file (def.site) for the synchrotron beam lines can be obtained from the beam line support staff.

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Last modified: April, 2005

Copyright © 2000-2005 HKL Research, Inc.