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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
- 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
在线留言
尊敬的客户朋友，如您有任何意见建议，请通过下表反馈给我们，我们会尽快与您联系。
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400-621-1085
