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FFJOIN (CCP4: Supported Program)NAMEffjoin - Fffear Fragment JOINing, release 1.0.0, 06/06/00SYNOPSISffjoin XYZIN foo.pdb [XYZIN1 foo.pdb] [XYZIN2 foo.pdb] XYZOUT bar.pdb REFERENCE
DESCRIPTION`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. `ffjoin' Recepiesffjoin xyzin alpha-helix-10-rot.pdb xyzout alpha-helix-10-rot-join.pdb << eof eof INPUT/OUTPUT FILESXYZINInput pdb file. This should contain a list of fragments output from `fffear'. XYZIN1Input pdb file. Additional fragments to be merged, e.g. from a different search model. XYZIN2Input pdb file. Additional fragments to be merged, e.g. from a different search model. XYZOUTOutput pdb file. This contains the CA coordinates for the merged fragments. The B-factors will contain updated confidence values which will be lower for those fragments which appear many times. KEYWORDSInput is keyworded. Available keywords are: JOIN, BUMP. BASIC KEYWORDS(All keywords are optional.) OUTPUTNew fragments are assembled using an internal numbering scheme from the input fragments which are described by their chain name and segid for the first input file only. Merged fragments are then eliminated by bumping according to their internal numbers. AUTHORKevin D. Cowtan, Department of Chemistry, University of York REFERENCES
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