Practical aspects of the integration of different software in protein structure solution.
There is presently an increasing variety of choice in the software for macromolecular phasing and automated model building. In addition to its positive features, this variety poses the problem of which software to use in a specific crystallographic case. Moreover, it must be decided whether a sequence of programs should be used to achieve structure solution more accurately and more rapidly, taking into account the features of the different programs: some software is more suitable for dealing with low-symmetry rather than high-symmetry space groups in the detection of heavy-atom sites, while others can give better estimates of the figures of merit on phases in certain cases (which is crucial in dealing with maximum likelihood) and others are more suitable for chain tracing at low/medium-low resolution than at high resolution or vice versa. The 'integrated' choice of different software has become popular among crystallographers, especially when facing crystallographic cases that are not straightforward. A few examples will be presented on the use of different programs to achieve the goal of structure solution and the associated practicalities that can make the difference between solving or not solving a structure.
Calderone
Vito
V
Department of Chemistry, University of Siena, Via Aldo Moro, 53100 Siena, Italy. vito.calderone@unisi.it
D001412:Bacillus subtilis / Q000201:enzymology; D003625:Data Collection; D003627:Data Interpretation, Statistical; D004926:Escherichia coli / Q000737:chemistry; D008668:Metallothionein / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013482:Superoxide Dismutase / Q000737:chemistry
D011506:Proteins; C007121:copper thionein; D008668:Metallothionein; D013482:Superoxide Dismutase