Appendix

 

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Installation Notes

 


Appendix - Installation notes

Downloading and unpacking HKL-2000 executable files

Executables of all programs can be obtained from our server hkl.hkl-xray.com. Please check our web page www.hkl-xray.com for the most recent information. 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). To download the programs, type the following instructions:

ftp hkl.hkl-xray.com

login: hkl2000ftp

password: The password can be obtained through the automatic password system (see WEB page) or by contacting HKL Research, Inc. via e‑mail. If you have successfully connected to the server you may type: 

ftp> ls

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

Linux:

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

>individual_programs (not tarred and not compressed)

MAC-INTEL:

> HKL2000_mac_0.###.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 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:

 

> get HKL2000_Macintel.###.tar.Z

 

After you've transferred 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

Installing HKL-2000

Typically the executables are placed in the directory:

/usr/local/bin

You can also place executables in arbitrary directory, for instance:

 

/home/joed/programs/hkl

In that case, you have to set environmental variable HKLPATH to that directory. The exact command will depend on the shell you are using to run programs (this can be determined by typing echo $SHELL). For the tcshell and the example above, the command is:

setenv HKLPATH /home/joed/programs/hkl

HKL-2000 requires also a directory hklint for site files. Its default location is:

/usr/local/hklint

(accessing it requires system privileges), but it can be changed to an arbitrary location, by setting the environmental variable HKLDIR. For example:

 setenv HKLDIR /home/joed/programs/hkl

 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 HKL

To 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).

 License key

Additionally the license key file, cr_info, needs to be present in the directory: 

/usr/local/lib

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 an info file. You may save the info file and afterwards 'manually' send it to hkl@hkl-xray.com.

 

Please:

ü       Do not edit or alter the info file - it is processed automatically after verification. 

ü       Do not send an info file as an attachment. 

ü       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!)

HOSTNAME: 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/MSC, HKL Research, etc.

VERSION: 0.98.696

Requested 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

un-brand - CCD Brandeis 2x2

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

Starting HKL-2000

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.

 

 

 

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