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HKL结构生物学软件包 HKL Research Inc.

 

HKL-2000已被100多家制药公司和1200多家学术,政府和非营利机构使用。 该软件也可用于许多同步加速器光束线。 描述该软件的论文在领先的科学期刊中引用了超过30,000篇,在有史以来最常被引用的前100篇科学论文中排名第23位。 据报道,在沉积到蛋白质数据库(PDB)的所有X射线晶体学结构中,超过50%用于结构测定过程。

HKL-3000软件将HKL-2000程序的所有功能与许多其他大分子晶体学计算机程序相结合:CCP4套件,ARP / wARP套件,SHELX-97套件,SOLVE / RESOLVE套件,Coot,PyMOL和Buccaneer。 已发表的550多篇论文报道了HKL-3000的使用。

HKL-2000

HKL-2000 program package is based on the extended versions of Denzo, XdisplayF and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc.

The software is driven by the graphical user interface, which greatly improves convenience of working with various data sets.

The package is distributed in form of the compiled executables. The supported operating systems are listed on Hardware & OS page.

Key Benefits

  • Due to 3-D processing, HKL-2000 can superbly handle data from crystals with very high mosaicity
  • It allows to process data collected with any spindle axis orientation and refine the direction of the spindle axis
  • Absorption correction dramatically improves anomalous signal
  • After processing and post-refinement the user can print-out a unified report with all statistics and graphs necessary for publication

HKL-3000

The most recent release of the HKL-3000 program distributed by HKL Research is the version 718.

The HKL-3000 users who have obtained their license directly from HKL Research can download the installer for the latest version from our server.

HKL-3000R users should contact Rigaku directly for information about the latest available version.

Reference to HKL-3000 Installation Hardware & OS

HKL-3000 interacts with many widely used programs like CCP4, SOLVE, RESOLVE, MLPHARE, SHELXD and SHELXE, ARP/wARP, DM, MOLREP, REFMAC, and MolProbity. These programs must be obtained directly from their respective authors or distributors.

References:

CCP4: Collaborative Computational Project,Number 4 (1994). Acta Cryst. D50, 760-763

SOLVE: Terwilliger, T. C. & Berendzen, J. (1999). Acta Cryst. D55, 849-861.

RESOLVE: Terwilliger, T. C. (2004).J. Synchrotron Rad. 11, 49-52.

MLPHARE: Otwinowski, Z. (1991). Proceedings of the CCP4 Study Weekend. Isomorphous Replacement and Anomalous Scattering, edited by W. Wolf, P. R. Evans & A. G. W. Leslie, pp. 80-86. Warrington: Daresbury Laboratory.

SHELXD: Schneider, T. R. & Scheldrick, G.M. (2002). Acta Cryst. D58, 1772-1779.

SHELXE: Scheldrick, G. M. (2002). Z. Kristallogr. 217, 644-650.

ARP/wARP: Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Nature Struct. Biol. 6, 458-463.

DM: Cowtan, K. (2001). Acta Cryst. D57, 1435-1444. Cowtan, K. & Main, P. (1998). Acta Cryst. D54, 487-493. Cowtan, K. D. & Zhang, K. Y. (1999). Prog. Biophys. Mol. Biol. 72, 245-270.

MOLREP: Vagin, A. A. & Teplyakov, A. (1997). J. Appl. Cryst. 30, 1022-1025. Vaguine, A. A., Richelle, J., Wodak, S. J. (1999). Acta Cryst. D55, 191-205.

REFMAC: Murshudov, G. N., Vagin, A. A. & D odson, E. J. (1997). Acta Cryst. D53, 240-255.

MolProbity: Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson and David C. Richardson (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66: 12-21. Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, W. Bryan Arendall III, Jack Snoeyink, Jane S. Richardson and David C. Richardson (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35: Web Server issue, W375-W383.

系统需求

Minimal Hardware Requirements
Memory 512MB or more
Swap Space 1.5GB or more
Graphics

16 bit or more graphics card, the optimal screen resolution is 1280 x 1024 or better, the minimal resolution is 1440 x 900.

Supported Operating Systems

HKL-2000 is available and was tested on the following platforms:

Linux
  • RedHat Enterprise Linux 4, 5, 6, and 7;
    32-bit and 64-bit versions,
  • RedHat Fedora 8 and higher;
    32-bit and 64-bit versions,
  • Ubuntu 8.04 LTS, 9.10, 10.04 LTS, 12.04 LTS, 14.04 LTS, 16.04 LTS
    32-bit and 64-bit versions,

RedHat distributions require installation of additional libraries:
>yum install xorg-x11-fonts-75dpi

Ubuntu distributions require installation of additional libraries:
>apt-get install xfonts-75dpi

Mac OS X (Intel based)
  • Mac OS X High Sierra (10.13)
  • Mac OS X Sierra (10.12)
  • Mac OS X El Capitan (10.11)
  • Mac OS X Yosemite (10.10)
  • Mac OS X Mavericks (10.9)
  • Mac OS X Mountain Lion (10.8)
  • Mac OS X Lion (10.7)
  • Mac OS X Snow Leopard (10.6)

Please note: The X11 server is not included in Mac OS X versions 10.8 and higher. Instead, the open source XQuartz server should be used. Please download the latest version of XQuartz (currently 2.7.9) from http://xquartz.macosforge.org and install it following the instructions on the site. For the 10.6 and 10.7 systems you may use either a default X server or an updated XQuartz server (specific to your system version).
Using Mac OSX 10.10 and 10.11, the initial rendering of each window is slow, but once the interface is loaded it works normally.Additionally, if the ‘Peak Search’ button on the Index page is used before the image has been displayed, the Xdisp window will close. The workaround for this is to first display the image using the use ‘Display’ button prior to performing a peak search.

Microsoft Windows 10

The HKL suites can be installed in Windows 10 (build 1703 or greater) by enabling the Windows Subsystem for Linux.Detailed instructions are provided here.

Older systems
For OSF 3.2, the last available version of HKL/HKL-2000 for OSF is 1.97.9. Due to the extinction of this OS, further support has been phased out.
For Irix 6.5 the last release is 0.98.695b. There will be no further support for this operating system.
软件限制

Scalepack limits for HKL-2000 version 708:

Program maxinh maxrej maxref mfpack ifitn
scalepack_lvirus 1000 300k 55M 10k 2*5001
scalepack (standard) 900 200k 16M 10k 2*5001
scalepack_mini 600 100k 16M 10k 2*5001
scalepack_micro 600 50k 2M 2k 2*1501

Scalepack limits for HKL-2000 version 704w to 707:

scalepack_lvirus: maxrej=200k, maxref=32M

Scalepack limits for HKL-2000 version 704u and earlier:

Program maxinh maxrej maxref mfpack ifitn
scalepack_16m 600 100k 32M 2k 2*1501
scalepack_8m 600 50k 8M 3k 2*3001
scalepack_manyframes 600 50k 2M 4k 2*2001
scalepack_mf6500 600 50k 3M 6.5k 2*3001
scalepack_virus 700 200k 32M 2.5k 2*2501
scalepack_lvirus 700 300k 50M 3k 2*3001
scalepack_ribo 700 200k 32M 2k 2*2001

maxinh- maximal h index

maxrej- maximal number of rejections

maxref- maximal number of reflections

mfpack- maximal number of frames

ifitn- maximal number of parameters that can be fitted simultaneously

Note:

Some versions do not exist on SGI due to limitations of SGI compiler to handle large memory requirements.

In case of problems with large versions, one should turn-off postrefinement.

HKL / HKL-2000 / HKL-3000软件认可的探测器和格式

HKL-2000/HKL-3000 recognizes over 300 detector formats. Due to the recent avalanche of new formats, we have decided to stop updating the list of detector models/formats below. If you have data that cannot be recognized by HKL-2000/HKL-3000, please contact us.

Detectors (frozen ~2015):
  • ADSC
    CCD ADSC Quantum-210
    CCD ADSC Quantum-270 - only in HKL-2000
    CCD ADSC Quantum-315
    CCD ADSC Quantum4 (all formats)
    CCD ADSC Quantum1 (all formats)
    CCD ADSC detector at CHESS - transformed data
  • APS CCD
    CCD APS-1 (all formats) - only in HKL-2000 package
    CCD SBC-2 (all formats) - only in HKL-2000 package
    CCD SBC-3 (all formats) - only in HKL-2000 package
  • Bruker
    CCD Bruker Smart6000 (all formats) - only in HKL-2000 package
    CCD Bruker Smart6500 (all formats) - only in HKL-2000 package
    CCD Bruker Smart2000 (all formats) - only in HKL-2000 package
  • Dectris
    Pilatus 6M - only in HKL-2000
    Pilatus 2M - only in HKL-2000
  • Mac Science
    MAC Science DIP-100 scanner
    MAC Science DIP-2000 scanner 12-bit A/D converter
    MAC Science DIP-2000 scanner 16-bit A/D converter
    MAC Science DIP-2030 scanner 12-bit A/D converter
    MAC Science DIP-2030 scanner 16-bit A/D converter
    MAC Science DIP-3000 cylindrical Weissenberg scanner
    MAC Science DIP-320 Weissenberg scanner
    MAC Science DIP-420 off-line scanner
  • MAR Research
    MAR CCD detector 130 mm
    MAR CCD detector 165 mm
    MAR CCD detector 225 mm - only in HKL-2000
    MAR CCD detector 300 mm - only in HKL-2000
    MAR CCD detector 325 mm - only in HKL-2000
    MAR scanner - 180 mm plate (uncompressed format)
    MAR scanner - 300 mm plate (uncompressed formats)
    MAR scanner - 345 mm plate (all formats, compressed and uncompressed)
    MAR scanner - at LMB Cambridge
    MAR prototype - Red scanner at EMBL in Hamburg
  • Nonius
    Nonius Kappa CCD detector (all formats) - only in DENZO-SMN package
  • Off-line scanners at Synchrotron Sources
    Film scanner - Purdue type
    Film scanner - Uppsala type
    Film scanner - Weizmann type
    fuji 10 bit scanner
  • Photon Factory
    FUJI 10bit off-line scanner
    FUJI BA-100 scanner at Photon Factory
    Fuji scanner at beam line18b at Photon Factory
  • Rigaku
    RAXIS-II Rigaku scanner (all formats)
    RAXIS-III (RAPID, SPIDER) - only in HKL-2000
    RAXIS-IV and RAXIS-IV++ Rigaku scanner (all formats)
    RAXIS-IV Rigaku scanner - prototype
    RAXIS-V
    RAXIS-HTC
    Saturn 724 - only in HKL-2000
    Saturn 92 - only in HKL-2000
    Saturn 944 - only in HKL-2000
    Saturn A200 - only in HKL-2000
    Screen Machine - only in HKL-2000
    Pilatus 200K - only in HKL-2000
  • Stoe
    Stoe scanner
  • Prototype CCD Detectors at Synchrotron Facilities
    CCD detector 55mm [original] 1k at CHESS - transformed data
    CCD detector 80mm 2k at CHESS - transformed data
    CCD detector - beam line 19 at ESRF
    Brandeis 1k CCD detector at X12C beam line at BNL
    Brandeis 2k CCD - mosaic at BNL
    Brandeis 2k CCD single chip detector at X12C beam line at BNL

Detector* XdisplayF Ver. 1.96 and higher Modifierand Denzo Format Modifier
ADSC
ADSC Quantum-210 CCD detector (corrected data) ccd adsc unsupported-q210(a)
ADSC Quantum-210 CCD detector (corrected data) binned ccd adsc unsupported-q210 binned(a)
ADSC Quantum-315 CCD detector (corrected data) ccd adsc unsupported-q315(b)
ADSC Quantum-315 CCD detector (corrected data) binned ccd adsc unsupported-q315 binned (b)
ADSC Quantum4 CCD detector (raw data) ccd adsc quantum4
ADSC Quantum4 CCD detector (raw data) dezingering-on ccd adsc quantum4 dz
ADSC Quantum4 CCD detector (raw data) binned ccd adsc quantum4 binned
ADSC Quantum4 CCD detector (raw data) binned dezingering-on ccd adsc quantum4 binned dz
ADSC Quantum4 CCD detector (corrected data) ccd adsc unsupported-q4
ADSC Quantum4 CCD detector (corrected data) binned ccd adsc unsupported-q4 binned
CCD (ADSC) detector single at CHESS ccd adsc
Detector XdisplayF Ver. 1.96 and higher Modifierand Denzo Format Modifier
APS CCD
CCD APS-1 detector at SBC ccd aps1
CCD APS-1 detector at SBC in binned mode ccd aps1 binned
CCD SBC-2 detector at SBC ccd sbc2
CCD SBC-2 detector at SBC in binned mode ccd sbc2 binned
CCD SBC-3 detector at SBC ccd sbc3
CCD SBC-3 detector at SBC in binned mode ccd sbc3 binned
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Bruker
CCD Bruker quad detector - IMCA beam line ccd bruker quad
CCD Bruker quad detector (binned mode) - IMCA beam line ccd bruker quad binned
CCD SMART-6000 Bruker detector ccd smart6000
CCD Bruker single detector (older) ccd bruker
CCD SMART-6000 Bruker detector in binned mode ccd smart6000 binned
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Mac Science
MAC Science DIP-100 dip 100
MAC Science DIP-2000 12-bit A/D converter dip 2020
MAC Science DIP-2000 16-bit A/D converter dip 2020b
MAC Science DIP-2030 12-bit A/D converter dip 2030
MAC Science DIP-2030 16-bit A/D converter dip 2030b
MAC Science DIP-2040 16-bit A/D converter dip 2040b
MAC Science DIP-3000 cylindrical Weissenberg dip 3000
MAC Science DIP-320 Weissenberg scanner dip 320
MAC Science DIP-320 Weissenberg scanner 16bit dip 320b
MAC Science DIP-3200 Weissenberg scanner dip 3200
MAC Science DIP-3200-2 Weissenberg scanner (long) dip 3200l
MAC Science DIP-420 off-line scanner dip 420
MAC Science DIP scanner for neutrons 0.2mm pixel dip nf
MAC Science DIP scanner for neutrons 0.4mm pixel dip nc
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
MAR Research
MAR CCD detector 165 mm ccd unsupported-m165
MAR CCD detector 130mm ccd unsupported-mar
MAR 345mm scanner 180mm scan 100 micron size mar345 180mm 100
MAR 345mm scanner 180mm scan 100 micron size compressed mar345 180mm 100 marpck
MAR 345mm scanner 180mm scan 150 micron size mar345 180mm 150
MAR 345mm scanner 180mm scan 150 micron size compressed mar345 180mm 150 marpck
MAR 345mm scanner 240mm scan 100 micron size mar345 240mm 100
MAR 345mm scanner 240mm scan 100 micron size compressed mar345 240mm 100 marpck
MAR 345mm scanner 240mm scan 150 micron size mar345 240mm 150
MAR 345mm scanner 240mm scan 150 micron size compressed mar345 240mm 150 marpck
MAR 345mm scanner 300mm scan 100 micron size mar345 300mm 100
MAR 345mm scanner 300mm scan 100 micron size compressed mar345 300mm 100 marpck
MAR 345mm scanner 300mm scan 150 micron size mar345 300mm 150
MAR 345mm scanner 300mm scan 150 micron size compressed mar345 300mm 150 marpck
MAR 345mm scanner 345mm scan 100 micron size mar345 345mm 100
MAR 345mm scanner 345mm scan 100 micron size compressed mar345 345mm 100 marpck
MAR 345mm scanner 345mm scan 150 micron size mar345 345mm 150
MAR 345mm scanner 345mm scan 150 micron size compressed mar345 345mm 150 marpck
red EMBL scanner in Hamburg mar_corr
MAR scanner @ LBL -LMB prototype 1187 pixel format mar lbl
MAR scanner in MRC-LMB compressed 'pck' mode mar compressed
MAR scanner in small plate mode mar 18cm
MAR scanner in large plate mode mar 30cm
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Nonius
Nonius KappaCCD detector ccd nonius
Nonius KappaCCD detector dezingering-on ccd nonius dz
Nonius KappaCCD detector binned ccd nonius binned
Nonius KappaCCD detector binned dezingering-on ccd nonius binned dz
Nonius KappaCCD-2000 detector ccd noniusb
Nonius KappaCCD-2000 detector dezingering-on ccd noniusb dz
Nonius KappaCCD-2000 detector binned ccd noniusb binned
Nonius KappaCCD-2000 detector binned dezingering-on ccd noniusb binned dz
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Off-line scanners at Synchrotron Sources
fuji 10 bit scanner 100 micron raster fuji 10bit
Film scanner (Purdue type) 25 micron scan film 25
Film scanner (Purdue type) 50 micron scan film 50
Film scanner (Purdue type) 100 micron scan film 100
Film scanner (Uppsala type) 50 micron scan film lars
Film scanner (Weizmann type) 50 micron scan film is
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Photon Factory
Photon Factory - Amemiya drum scanner pf beam line 14a
Photon factory fuji BA-100 scanner NL format fuji nl
Photon factory fuji BA-100 scanner NL format (Weisenberg exp) weis nl
Photon factory fuji BA-100 scanner SL format (Weisenberg exp.) weis sl
Photon Factory beam line 18b whole image pf beam line 18b
Photon Factory beam line 18b center pf beam line 18b center
Photon Factory beam line 18b beam region pf beam line 18b beam
Photon Factory beam line 18b bottom pf beam line 18b bottom
Photon Factory beam line 18b top pf beam line 18b top
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Rigaku
RAXIS-IIc Rigaku scanner 105 micron raster scan raxis
RAXIS-IIc Rigaku scanner 210 micron raster scan raxis 210
RAXIS-IIc Rigaku scanner 105 micron raster scan (Japanese version) raxis2n
RAXIS-IIc Rigaku scanner 210 micron raster scan (Japanese version) raxis2n 210
RAXIS-III Rigaku scanner raxis3s(a)
RAXIS-III Rigaku scanner raxis3s wide (a)
RAXIS-IV Rigaku (prototype) 100 micron raster scan raxis4 old
RAXIS-IV Rigaku scanner 50 micron raster scan raxis4 50
RAXIS-IV Rigaku scanner 100 micron raster scan raxis4 100
RAXIS-IV Rigaku scanner 200 micron raster scan raxis4 200
RAXIS-V Rigaku scanner 100 micron raster scan raxis5 100 (a)
Saturn 724 - only in HKL-2000
Saturn 92 - only in HKL-2000
Saturn 944 - only in HKL-2000
Saturn A200 - only in HKL-2000
Screen Machine - only in HKL-2000
Pilatus 200K - only in HKL-2000
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Stoe
STOE scanner stoe
Detector XdisplayF Ver. 1.96 and higher Modifier and Denzo Format Modifier
Prototype CCD Detectors at Synchrotron Facilities
CCD (Brandeis University) at BNL X12c ccd brandeis
CCD Brandeis 2x2 ccd unsupported-b4
CCD Brandeis 2 single chip detector at X12C beam line at BNL ccd unsupported-b4
CCD detector EEV chip 576 pixels ccd eev 576
CCD detector EEV chip 576 pixels double image mode ccd eev 576 double
CCD detector EEV chip 620 pixels ccd eev 620
CCD detector EEV chip 621 pixels ccd eev 621
CCD detector EEV chip 625 pixels ccd eev 625
CCD detector EEV chip 625 pixels binned ccd eev 625 binned
CCD detector EEV chip 1152 pixels ccd eev
CCD (ESRF) detector (BL19 at ESRF- raw data) ccd bl19
CCD (ESRF) detector (BL19 at ESRF>1200x1200) pxl)) ccd esrf fit2d transformed
CCD (ESRF) detector (BL19 at ESRF>1200x1200) pxl)) ccd esrf fit2d transformed wrong distance
CCD (ESRF) detector 1024*1024 ccd esrf 1024
CCD (ESRF) detector 1152x1242 ccd esrf 1242
CCD 1k 55mm [original Sol Gruner] detector at CHESS ccd chess 55mm
CCD 2k detector CHESS 2048x2048 image ccd chess 80mm
CCD 2k detector CHESS 1024x1024 (binned mode) ccd chess 80mm binned

* Due to various vendor policies, the detector format depends more on the vendor (or sometimes the beamline) than on the manufacturer’s model name.

The HKL package version - 1.97.0

The HKL package version - 1.97.2

 

 

 

 


 

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