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Crank specifications

Information


Unique identifier OMICS_28068
Name Crank
Alternative name CRANK2
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No
Wikipedia http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_experimental_phasing_with_Crank

Documentation


Maintainers


This tool is not available anymore.

Additional information


https://www.ccp4.ac.uk/ccp4online/ http://www.bfsc.leidenuniv.nl/software/crank/index.html http://www.ccp4.ac.uk/html/crank.html

Publication for Crank

Crank in pipelines

 (6)
2017
PMCID: 5370187
PMID: 28347402
DOI: 10.7554/eLife.21465.039

[…] with xds (), and further scaling and merging was pursued with the ccp4 suite () (rrid:scr_007255). the structure was solved by the sad method from peak-data collected from semet crystals. the crank2 pipeline () was used for structure solution and initial model building. refinement was carried out with phenix () (rrid:scr_014224). data collection and refinement statistics are summarized […]

2017
PMCID: 5698469
PMID: 29162826
DOI: 10.1038/s41467-017-01832-6

[…] the data were scaled using scala within the ccp4 suite of programs. prephadata was used to convert the mtz to shelxs format and shelx_cde was used to identify the se subsites through sad. finally, crank was used to construct the initial model of zgal_3152 through substructure refinement and model building. this model was then used to solve the structure of the native zgal_3152 by molecular […]

2017
PMCID: 5765458
PMID: 29083543
DOI: 10.1111/febs.14310

[…] with xscale , before merging with aimless . a high resolution cut‐off was selected based upon the resolution at which the anomalous signal became unusably weak. the merged data were fed into the crank2 pipeline , using sftools, shelxc and d , refmac5 , mapro, solomon , multicomb, parrot and buccaneer . the number of trials or cycles for several steps was significantly increased […]

2016
PMCID: 4784662
PMID: 26960118
DOI: 10.1107/S2059798316000401

[…] intensity of synchrotron beams coupled with pixel-array detectors allow data to be collected in minutes, software pipelines [autosol (terwilliger et al., 2009), autosharp (vonrhein et al., 2007), crank2 (skubák & pannu, 2013), hkl-3000 (minor et al., 2006) and shelxc/d/e (sheldrick, 2010)] can assess each data set in minutes, and beamline robotics allow many samples to be evaluated […]

2016
PMCID: 5031297
PMID: 27655155
DOI: 10.1186/s12915-016-0303-0

[…] by imosflm and data was scaled using scala with the anomalous pairs separated to enable calculation of anomalous difference maps for the zinc containing crystals [, ]. data were then input into the crank2 pipeline component of the ccp4 online programs []. in brief, free set was defined using sftools; followed by heavy atom structure factors (fa) estimation by shelxc; substructure determination […]


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Crank in publications

 (42)
PMCID: 5923425
PMID: 29703953
DOI: 10.1038/s41467-018-04142-7

[…] data sets were selected using a genetic algorithm that maximised the anomalous signal while retaining acceptable merging r-values. these data sets were merged in xscale and submitted to the crank2 pipeline in combination with the native data set for substructure determination and phasing by siras. the resulting map was used for automatic model building with buccaneer followed […]

PMCID: 5876331
PMID: 29599493
DOI: 10.1038/s41467-018-03498-0

[…] subsequently processed, integrated and scaled using mosflm/scala. the statistics of the data collection are shown in supplementary table . single wavelength dispersion (sad) method implemented in crank2 was used to phase pml ring. eight zn2+ positions were determined by crunch2 using data between 20 and 1.6 å. an interpretable map was obtained by solvent flattening using program solomon. […]

PMCID: 5851990
PMID: 29540701
DOI: 10.1038/s41467-018-03460-0

[…] facility (beamline id29) at 100 k. to maximise anomalous signal, data were collected at the l-iii pt edge (λ = 1.072 å). data were processed as above, but bijvoet pairs were unmerged (table ). crank2, was used to calculate phases and build an initial model. the model was manually improved using coot and the nhl domain was placed by molecular replacement in phaser using a modifed […]

PMCID: 5947703
PMID: 29497021
DOI: 10.1107/S2053230X18002236

[…] to structure factors using ctruncate (french & wilson, 1978) as implemented in ccp4 (winn et al., 2011). using the scaled data, a partial structure solution was obtained using the automated crank2 pipeline (skubák & pannu, 2013) in ccp4. the structure was then refined using refmac5 (murshudov et al., 2011) from ccp4 and phenix.refine (afonine et al., 2012) from phenix (adams et al., […]

PMCID: 5892559
PMID: 29449376
DOI: 10.1074/jbc.RA118.001796

[…] symmetry was applied to locate the corresponding helices in the asymmetric unit. the anomalous substructure and the initial model of the asymmetric unit comprising eight helices were fed to crank2 () to produce improved maps benefiting from 4-fold averaging and an almost complete model., complete high-resolution data from for semet-labeled crystals of ssek3(14–333) were collected […]


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Crank institution(s)
Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
Crank funding source(s)
Supported by the N.W.O.

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