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CCP4i: Graphical User Interface |
| Model Building Module |
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The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.
Buccaneer performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.
The target distributions are generated by a simulation calculation using a known 'reference' structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved, 'work' structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure.
In this task, rounds of chain-tracing with Buccaneer are alternated with rows of refinement using Refmac, to attempt to autobuild the structure. For chain-tracing only, use the Fast build only interface.
See program documentation: BUCCANEER, REFMAC5.
Buccaneer performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. For information on the use of 'reference' structures, see above.
In this task, only chain-tracing is performed. For chain-tracing alternated with refinement, see the Autobuild/Refine task.
See program documentation: BUCCANEER.
Rapper performs conformer modelling through sampling residue specific phi/psi propensity tables and rotomeric states given a set of restraints.
Documentation on using Rapper through CCP4i can be found as part of the Rapper documentation.
See program documentation: RAPPER.
Sequins performs sequence validation by comparing the model side chains against the electron density. It may be run with phases from experimental phasing, or it can calculate its own phases using a side-chain-omit process. In this case it can be used after molecular replacement, or to validate structures in the PDB.
See program documentation: SEQUINS.
FFFear - Fast Fourier Feature Recognition for density fitting.
FFFear is a package which searches for molecular fragments in poor quality electron density maps. It was inspired by the Uppsala 'ESSENS' software, but achieves greater speed and sensitivity through the use of Fast Fourier transforms, maximum likelihood, and a mixed bag of mathematical and computational approaches. Currently, the main application is the detection of helices in poor electron density maps (5.0Å or better), and the detection of beta strands in intermediate electron density maps (4.0Å or better). It is also possible to use electron density as a search model, allowing the location of NCS elements. Approximate matches may be refined, and translation searches may be performed using a single orientation.
The program takes as input an MTZ file containing the Fourier coefficients of the map to be searched, and a search model in the form of a pdb file, map, or maximum likelihood target. A 'fragment mask' is generated to cover the fragment density, and orientations and translations are searched to find those transformations which give a good fit between the fragment density and map density within the fragment mask.
The program has been highly optimised using reciprocal-space rotations and grid-doubling FFT's, and crystallographic symmetry giving 4-50 times speed improvement over the results published in 1998. The speed of the calculation is almost independent of the size of the model, thus the program may also be used for molecular replacement calculations where weak phases are available.
Features to look out for in the FFFear Task are:
| Folder title | Importance | Comment |
|---|---|---|
| Solvent Content | Use solvent fraction | Requirement for running the program |
See program documentation: FFFEAR.
FFJoin - Fffear Fragment JOINing.
FFJoin takes files of fragments output from FFFear and merges linked fragments to create longer fragments (with greater confidence values). Fragments running in opposite directions may optionally be merged. Overlapping fragments which cannot be merged may optionally be identified and the fragment with the lower confidence value removed. Since fragments of opposite direction may be merged, the output file will only contain alpha Carbons.
FFJoin does not know about crystal symmetry or repeat, so all input fragments should be calculated in FFFear using the same CENTRE keyword.
See program documentation: FFJOIN.
This is a launcher for the XtalView package which is NOT distributed by CCP4. The interface will extract the crystal data from any PDB or map file selected (and use that from the last file selected) to create an xfit crystal file (project_dir/n_xfit_xfit.xtal) where project_dir is the project directory and n is the job number. The script will convert the CCP4 map files to xfit .fs files and create a xfit macro file (project_dir/n_xfit.script) which contains the commands to load the .fs files and PDB files. CCP4i will then start XtalView.
See program documentation: XtalView.
See also:
WWW O - The official
WWW server for users of the O protein crystallographic package.
QUANTA.
XtalView - A complete package for solving a macromolecular
crystal structure by isomorphous replacement, including building the molecular model.
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