Limits...
BALBES: a molecular-replacement pipeline.

Long F, Vagin AA, Young P, Murshudov GN - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: It uses a reorganized database taken from the PDB with multimeric as well as domain organization.A system manager written in Python controls the workflow of the process.Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

View Article: PubMed Central - HTML - PubMed

Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, Heslington, York, England.

ABSTRACT
The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from the PDB with multimeric as well as domain organization. A system manager written in Python controls the workflow of the process. Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

Show MeSH
BALBES ccp4i interface.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2394813&req=5

fig4: BALBES ccp4i interface.

Mentions: Fig. 4 ▶ shows an example of the ccp4i-style interface. The user only needs to provide a sequence and an experimental data file. Although the input is sufficiently simple, the output files contain all the process information, including the results of the analysis of the data by SFCHECK, REFMAC and MOLREP. If a solution is found, then a PDB file and an MTZ file containing the weighted coefficients corresponding to the refined models are also given.


BALBES: a molecular-replacement pipeline.

Long F, Vagin AA, Young P, Murshudov GN - Acta Crystallogr. D Biol. Crystallogr. (2007)

BALBES ccp4i interface.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394813&req=5

fig4: BALBES ccp4i interface.
Mentions: Fig. 4 ▶ shows an example of the ccp4i-style interface. The user only needs to provide a sequence and an experimental data file. Although the input is sufficiently simple, the output files contain all the process information, including the results of the analysis of the data by SFCHECK, REFMAC and MOLREP. If a solution is found, then a PDB file and an MTZ file containing the weighted coefficients corresponding to the refined models are also given.

Bottom Line: It uses a reorganized database taken from the PDB with multimeric as well as domain organization.A system manager written in Python controls the workflow of the process.Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

View Article: PubMed Central - HTML - PubMed

Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, Heslington, York, England.

ABSTRACT
The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from the PDB with multimeric as well as domain organization. A system manager written in Python controls the workflow of the process. Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

Show MeSH