Jiffies
Jiffies are small utilities written to perform (generally) a single functionality such as reformatting an .hkl file to an XPLOR .fobs file. We have a great many of these written both locally and from throughout the crystallographic community. Some of those with which I am familiar have been relocated to /public/apps/bin on the SGI's. A subset of the more useful are briefly described below.
- 4d_xdldataman - a semi-GUI driven version of the 'O' utility 4d_dataman
- 4d_xdlmapman - a semi-GUI driven version of the 'O' utility 4d_mapman
- sginfo - gives you everything you need to know about your space group
- renumberpdb - does exactly that
- resetb - Again, just what is says - resets the B-factors of a .pdb file to 15.00
- xplorhkl - reads in a .hkl file and writes out a .fobs file
- doitall - A semi-complete set of utilities that perform most of the .pdb manipulations one needs to do every day during refinements. Very useful. Supercedes the three jiffies above. Includes:
- Renumber atoms
- Renumber residues
- Renumber atoms & residues
- Remove hydrogens
- Difference map peak picker
- Split apart .pdb file for XPLOR
- Analyze structure geometry
- Generate luzzati list
- Compare 2 .pdb files
- Calculate model dimensions
- Reset B-factors
- prostat - a program for looking at structural information such as:
- Calculates MW and F(000)
- Calculates and lists average B-values
- Calculates protein torsion angles throughout
- Calculates geometry for non-protein groups
- Calculates intra-molecular hydrogen bonds
- Calculates inter-molecular hydrogen bonds
- Calculate crystal contacts
- Calculate intramolecular contacts for ligands
- mtz2f - converts a CCP4 .mtz format file to ascii
- pickwater.csh - a modified (by me) script from Sweden for automatically picking
peaks out of difference maps, caveat emptor! - waterconverter.awk - an awk script by our own C.Sage for converting the
output of 'pickwater' into something readable by XPLOR - reorder.awk - an .awk script for reindexing P6(3) ecTS .hkl data
- xplor2hkl.awk - an awk script for converting XPLOR .fobs files to .hklF
- denzo_to_fobs.awk - an awk script for converting denzo .hklI data to .hklF
- do_Isc2mtz generates .mtz and .fob format files from a SCALEPACK .hkl file. It's integrated into our CCP4 installation.
Return to the MSG Local Programs Page (up one level).
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