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Buccaneer specifications

Information


Unique identifier OMICS_32846
Name Buccaneer
Alternative name BUild Connected C-Alphas, Nautical Excuse for Eponym Required
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.5
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kevin Cowtan

Additional information


http://www.ysbl.york.ac.uk/~cowtan/buccaneer/cbuccaneer.html

Publication for BUild Connected C-Alphas, Nautical Excuse for Eponym Required

Buccaneer citations

 (417)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] d using as a template the previously reported EndoS structure (unmodified PDB 4NUZ) and molecular replacement methods implemented in Phaser and the PHENIX suite. Model rebuilding was carried out with Buccaneer and the CCP4 suite. The final manual building was performed with Coot and refinement with phenix.refine. The structure was validated by MolProbity. Data collection and refinement statistics […]

call_split

Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications

2018
PMCID: 5941314
PMID: 29626159
DOI: 10.1042/BCJ20170909
call_split See protocol

[…] INTLESS from the CCP4 software suite []. The anomalous signal of Zn2+ atoms was utilized for initial SAD phasing of the Ube2N : ZNRF1CTD crystal using the SHELX suite [] and the model was built using BUCCANEER []. Subsequent rounds of manual building and refinements were carried out using COOT [], REFMAC5 [], and Phenix.Refine []. […]

call_split

Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin dockerin interaction

2018
Sci Rep
PMCID: 5934362
PMID: 29725056
DOI: 10.1038/s41598-018-25171-8
call_split See protocol

[…] .0% and the dockerins between 22% (Doc3) and 34% (Doc1b). Two copies of the heterodimer RfCohScaB5-DocScaA complex were present in the asymmetric unit. The partially obtained model was completed with Buccaneer and with manual modeling in COOT. It was then refined using REFMAC5 and PDB REDO interspersed with model adjustment in COOT. The final round of refinement was performed using the TLS/restrai […]

library_books

Structural analysis of human ARS2 as a platform for co transcriptional RNA sorting

2018
Nat Commun
PMCID: 5923425
PMID: 29703953
DOI: 10.1038/s41467-018-04142-7

[…] n 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 by iterative rounds of manual building and refinement with REFMAC5. The well-defined selenomethionine positions were used as sequence markers (Supplementary Fig. ).Subsequent ARS2 s […]

library_books

Bacteroides thetaiotaomicron generates diverse α mannosidase activities through subtle evolution of a distal substrate binding motif

2018
Acta Crystallogr D Struct Biol
PMCID: 5930347
PMID: 29717710
DOI: 10.1107/S2059798318002942

[…] y et al., 2007) with the coordinates of a previously solved Bt GH92 enzyme, BT3990 (PDB entry 2wvy; Zhu et al., 2010), as a phasing model. Initial atomic models of both enzymes were constructed using Buccaneer (Cowtan, 2006) and were extended by iterative rounds of manual model building and refinement using Coot (Emsley et al., 2010) and REFMAC (Murshudov et al., 2011). For the ligand-bound struct […]

library_books

A new family of periplasmic binding proteins that sense arsenic oxyanions

2018
Sci Rep
PMCID: 5908839
PMID: 29674678
DOI: 10.1038/s41598-018-24591-w

[…] ata were collected from one SeMet-AioX crystal and processed with CCP4 software. The MTZ reflection file obtained was used to determine the position of five selenium atoms through SHELX C/D/E (CCP4). BUCCANEER was used to generate the AioX model. The final AioX model was generated through interactive cycles of model building in Coot and a restrained refinement routine in REFMAC5. The structures of […]

Citations

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Buccaneer institution(s)
Department of Chemistry, University of York, Heslington, UK
Buccaneer funding source(s)
Supported by The Royal Society under a University Research Fellowship.

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