CPP4

CCP4 (Collaborative Computational Project No. 4; http://www.ccp4.ac.uk/) is a suite of software for macromolecular X-ray crystallography.

It contains several important software for X-ray crystallography, including

CCP4 7.0 is installed on Aurora.
To use it, you need to add the following line to you .bash_profile:
. /lunarc/nobackup/projects/bio/CCP4/ccp4-7.0/bin/ccp4.setup-sh

You can easily install it for other computers.
The description below applies to the version on Macintosh.


Working with Coot

Sometimes, Coot does not read the pdb file
writing the line
allow_duplicate_sequence_numbers()
into the file $HOM/.coot-preferences/startup.py
may solve the problem


Maps



Model building in Coot
The right-hand side of the Coot window has a lot of useful tools for model building.



Looking at electron-density maps with Coot

Can be done in 3 ways

Simplest is to load the precompiled map from EDS:
  1. Open Coot
  2. Select File - Fetch PDB&map using EDS
  3. Enter PDB Code

Download mtz file with Phenix

  1. Run on command line
    phenix.fetch_pdb --mtz pdb_id
    This gives a mtz file without any map
  2. phenix.maps mtz_file pdb_file
    This calculate the maps, which are 2Fo-Fc and Fo-Fc by default.
  3. This map file (in mtz format) can be opened in Coot, command Auto Open MTZ


This can be done with Phenix's graphical interface (but normally more complicated):

  1. Reflection tools - Reflection file editor
    Enter file
    Mark intensity or Amplitude and click on +
    Do the same thing for refln.status (type unknown)
    Output options
    Untick generate R-free flags
    Set name of file
    If errors, go back to Data Selection and then click on output arrays and change output column labels to "IOBS" "SIGIOBS" also for Rfree
  2. Maps - Model-based maps
    Model file: pdb
    Reflection file: mtz
    When maps are calculated, you can see R and Rfree in the output file.
    The results are always put in a new directory.

Download cif file from PDB

  1. Find the PDB code on https://www.rcsb.org
  2. Download Files - Structure Factors (CIF)
  3. phenix.cif_as_mtz cif_file
    This gives an mtz file of the structure factors
  4. phenix.maps mtz_file pdb_file


Neutron maps

  1. Download pdb and structure factors from PDB
    phenix.cif_as_mtz 6eym-sf.cif
  2. Phenix - Reflection file editor
    Read in the new mtz file and select the proper X-ray and neutron intensities/amplitudes and R-free flags
  3. Then make maps in two steps (Model-based maps)
    Scattering table n_gaussian for X-ray
    Scattering table neutron for neutron maps



cif files
Avogadro can open cif files, but it opens a single assymetric unit that may not show the full molecule.
Mercury from CCP4 works much better.

File formats


Structure factors
cif
cns
viewHKL

Maps
mtz (map coefficients, bin; can be read by Phenix, Coot, edstat; pdb_fmodel.mtz pdb_map_coeffs.mtz)
cube (QM, form)
dx (VMD, form)
NA4 (map, form but coded in letters; maptona4)
dsn6 (bin from PDB; can be read by Pymol)
map (bin)
ccp4 (bin, can be read by Pymol)
fs4 (XtalView; map2fs)

mapdump
maptona4 forth and back between ccp4 and na4 maps
mapexchange
peakmax
mapman and xdlmapman:
Supported input formats : PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR EZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK
Supported output formats : CCP4 EZD MASK NEWEZD ENVELOPE


Reflections (structure factors)
Convert Xplor or CNS reflections to mtz: f2mtz (CCP4) or combat.
Convert mtz to cif: mtz2cif (CCP4)
Convert mtz to other formats (e.g. Xplor/CNS,cif): mtz2various (CCP4)