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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.
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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