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cctbx specifications


Unique identifier OMICS_15604
Name cctbx
Alternative name Computational Crystallography Toolbox
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License Other
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes


No version available


  • person_outline Paul Adams

Publication for Computational Crystallography Toolbox

cctbx citations


A convolutional neural network based screening tool for X ray serial crystallography

J Synchrotron Radiat
PMCID: 5929353
PMID: 29714177
DOI: 10.1107/S1600577518004873

[…] Several open-source software packages are available for automatic hit-finding performed on XFEL data, including Cheetah (Barty et al., 2014) and cctbx.xfel (Sauter et al., 2013). Within the cctbx.xfel package, automatic spot picking algorithms used for hit-finding are implemented within both the CCTBX (Zhang et al., 2006) and DIALS (Winter et […]


Determination of Patterson group symmetry from sparse multi crystal data sets in the presence of an indexing ambiguity

Acta Crystallogr D Struct Biol
PMCID: 5930348
PMID: 29717711
DOI: 10.1107/S2059798318002978

[…] The maximum possible lattice symmetry compatible with the averaged unit cell is determined using algorithms based on ideas by Le Page (1982) and Lebedev et al. (2006), and implemented in cctbx (Grosse-Kunstleve et al., 2004; Sauter et al., 2006). Subsequently, a list of all permissible symmetry operations is compiled. The Pearson’s correlation coefficient between data sets i and j, af […]


KAMO: towards automated data processing for microcrystals

Acta Crystallogr D Struct Biol
PMCID: 5930351
PMID: 29717715
DOI: 10.1107/S2059798318004576

[…] itaroyam/yamtbx/wiki. In this section, some processing examples are presented using the methods described here. The program versions used here were yamtbx commit 1107fc4 (as of 26 December 2017) with cctbx commit 16b2e7c (as of 17 April 2017); XDS 1 May 2016 (BUILT=20160617); CCP4 7.0 (update 042); PHENIX 1.11.1; SHELXC, SHELXD and SHELXE 2016/1, 2013/2 and 2016/3, respectively; and R 3.2.2. For d […]


Structural characterization of a highly potent V3 glycan broadly neutralizing antibody bound to natively glycosylated HIV 1 envelope

Nat Commun
PMCID: 5871869
PMID: 29593217
DOI: 10.1038/s41467-018-03632-y

[…] a 5-µm beam focus at the crystal interaction point. Diffraction images were recorded on a Rayonix MX325 detector data and were integrated with IOTA using the data reduction algorithms implemented in cctbx.xfel. Of the 627 collected images, 589 contained discernible diffraction; of these, 570 were successfully integrated and yielded correct crystal symmetry and unit cell values. Scaling, post-refi […]


CAPOW: a standalone program for the calculation of optimal weighting parameters for least squares crystallographic refinements

J Appl Crystallogr
PMCID: 5822994
PMID: 29507551
DOI: 10.1107/S1600576717016600

[…] The optimal weighting calculation is based upon a script from the computational crystallographic toolbox (cctbx; Grosse-Kunstleve et al., 2002). The cctbx is open source and freely available to download and alter. To enable easier modification and adaptation, the cctbx-dependent functions were rewritten t […]


CCP4i2: the new graphical user interface to the CCP4 program suite

Acta Crystallogr D Struct Biol
PMCID: 5947771
PMID: 29533233
DOI: 10.1107/S2059798317016035

[…] and can be intimidating or tedious to operate for many users. Although xia2 is itself primarily a command-line program, it has a structured interface for optional parameters using the Phil syntax of cctbx ( This interface is rich enough to describe the basic components of a GUI, including parameter types, tooltips, help strings and expert levels. It […]


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cctbx institution(s)
Lawrence Berkeley National Laboratory, Berkeley, CA, USA
cctbx funding source(s)
This work was funded in part by the US Department of Energy under Contract No. DE-AC03-76SF00098 and by NIH/ NIGMS under grant number 1P50GM62412.

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