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.
| Current Versions: | |
| Linux | HKL2000_linux_ver_0.98.699a |
| SGI | HKL2000_sgi_ver_0.98.695b |
| MAC OS X (Intel) | HKL2000_MacIntel_0.98.699f |
| MAC OS X (Power PC) | HKL2000_MAC_692i |
| OSF | HKL2000_osf_ver_0.97.647d |
You may download the HKL-2000 program executables from our ftp server hkl.hkl-xray.com. You may use a graphical ftp application, or use "ftp" command from a terminal window (to open a terminal window in MAC OS X, open the Finder's Go menu, choose Applications, then choose Utilities and select Terminal).
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_programsSGI:
> 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.
To download the appropriate file, e.g. HKL2000_Macintel.###.tar.Z use the get command. For example:
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 Typically the executables are placed in the directory: /usr/local/bin (requires system administrator privileges). You can also place the executables in an arbitrary directory, for instance
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 (this can be determined by typing echo $SHELL). For the tcshell and the example above, the
command is:
HKL-2000 requires also a directory hklint for site files. Its default location is:
> get HKL2000_Macintel.###.tar.Z
anomalous
cdir_t
denzo
denzo_3d
HKL2000
hklfilename
hklsysinfo
readheader
scalepack
scalepack16m
scalepack8m
scalepacklvirus
scalepackmanyframes
scalepackmf6500
scalepackribo
scalepacktest
scalepackvirus
strat
suser
xdark
xdisp
Installing HKL-2000
/home/joed/programs/hkl
setenv HKLPATH /home/joed/programs/hkl
/usr/local/hklint
(accessing it requires system privileges), but it it can be changed to an arbitrary location, by setting the environmental variable HKLDIR. For example:
setenv HKLDIR /home/joed/programs/hklint
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
You can check how the environmental variables were set by typing the command:
env | grep HKLTo keep the values of the HKL environmental variables for subsequent logins, you should modify the configuration files for the shell you are using (~/.tcshrc, ~/.cshrc, or ~./bashrc).
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):
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:
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 University | Licensee's Institution name |
| PI: John Doe | Principal Investigator or Group Leader |
| CONTACT: Jane Doe | Contact Person |
| DETECTORS: mar raxis4 | Detector Format Families |
| NO-OF-DET: 2 | Number of Detectors at Home Laboratory |
| PROVIDER: HKL | License Provider: Rigaku Americas Corporation, HKL Research, etc |
| VERSION: 0.98.689 | Requested Version of the Program |
| EXPIR: noexpir |
The following are detector families to be used in the above "questionnaire":
After you have installed HKL-2000 and placed the access file, cr_info, in /usr/local/lib directory, the program can be started from a terminal window by typing:
HKL2000
If you receive an error message "no display name and no $DISPLAY environment variable", it means that the X windows system is not working or not configured properly. On Mac OS X, you need to start the X11 application (from the Finder's Go menu, choose Applications, then choose Utilities and select X11). You should see the X11 icon in the dock, double click on it to open an xterm window and start HKL2000 from this window.
If you receive an error message "Command not found", it means that HKLPATH is not in the executable command search path. Modify the environmental variable PATH or type a full path e.g. /usr/local/bin/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.
Last modified: April, 2005
Copyright © 2000-2005 HKL Research, Inc.