CPP4

• Coot
• Refmac
• SHELX
• edstats

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.

• File - Open Coordinates (read pdb file)
• File - Open Map (read map in ccp4 format; you need to read in 3 maps)
  alternatively and easier, you may use
  File - Auto Open MTZ on the pdb_map_coerrs.mtz file
  
  
• You need to have a mouse with a central wheel
• Left button rotates
• Centre button translate and allows you to centre on some atom
  
• Right button zoom in or out
  
• Go to atom (small symbol on the top) helps you navigate through the protein. Middle click to centre on that atom. Space – next residue. Shift-space – previous residue.
  
  
• To show symmetry-related atoms:
  Draw - Cell & Symmetry - Symmetry On

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

• Display Manager shows all loaded maps and PDB files, and which map to scroll with the wheel. You can also change colors (properties) and delete objects here.
• https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/crib-sheet.pdf give additional data
• Scroll to change the sigma level of a map. The level is shown on the top of the screen.
  RMSD is the level in sigma.
  The default is 1.5 sigma for 2Fo-Fc and 3.0 sigma for Fo-Fc maps.
  
• In the difference map (Fo-Fc), positive density, green, is too little electron density (i.e. an atom should be there that is not), negative density, red, means too much electron density (i.e. an atom is there that shouldn’t be there).
• Higher sigma levels show a stronger signal

• Edit chi angles/torsion for manually changing the conformation of a residue
• Add alternate conformation: you can view different alternate conformers of a residue and choose which one to build in
• Place atom at pointer: useful for adding water molecules
• Escape button is useful if you got stuck in some processes (the windows sometimes disappear)
  
• Real-space refine zone
• Delete atoms
• Add water
  

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

• EDS never works.
• Be careful with phenix.cif_as_mtz! Neutron data usually contain both neutron and X- ray data and the program will not know which is which.
  Manually check the cif file and construct an mtz file from the GUI
• When building the maps, you need to build two separate map files:
  neutron, using the neutron scattering dictionary
  X-ray using the X-ray scattering dictionary.

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
   
   

File formats