Edit

• "Map Color", set up the color for the select map

Calculate

• "Model/Fit/Refine", same as the menu in the right window
  • "Map", select map
  • "Rotamer", choose the rotamer which can fit the density map best
  • "Real Space Refine Zone", refine the rotamer
  • "Regularize Zone", idealize model geometry
  • "Rigit Body Fit Zone", fix the select fragment
  • "Rotate Translate Zone", rotate and translate atoms by selecting two atoms
  • "Edit Chi Angles", adjust Chi angles
  • "Edit Backbone Torsions", adjust Phi and Psi according to the Ramachandra plots
  • "Add Alt Conf", add alternative conformation
  • "Delete", delete the selected residues

Draw

• "Go to Atom", centre selected atom and display the density map around it, use "Next Residue" and "Previous Residue" to move along the chain
• "Display Manager", “Scroll” button allows to select which map is affected by this
• "Sequence View", view the sequence
• "Clipping", set up the diplay depth
• "Cell & Symmetry", Display Symmetry Atoms

Measure

• "Distances & Angles", measure distance, angles, torsion angles
• "Environment Distances", display the hydrogen bonds and bumps
• "Clean Atom Labels", remove the atom labels created by "Shift+Left Button"

Validate

• "Density Fit Analysis", density fit metrics
• "Unmodelled Blobs", find the unexplained density blobs

1. "Rotamer", choose the rotamer fiting the density map best
2. "Real Space Refine Zone", refine the selected residue

1. "Validate -> Unmodelled Blobs", find the unexplained density blobs
2. "Place Atom At Pointer", place atoms to the selected density blob
3. "File -> Seach Monomer library", search and insert monomer
4. "Calcualte -> Fit Loop ... Fit Loop by Rama Search", add missed residues

Comparing the NCS related electron density

• "Calcualte -> NCS maps

Comparing the NCS-related chains

• "Draw -> NCS ghost control

Compare the NCS-related chains using “NCS jumping”

• "o", Other NCS-related chain

Comparing the Ramachandran plots for related chains

• "Validate -> Kleywegt plot

"Delete", remove the residue

"Calculate -> Fit Loop", add ALA residue

"Mutate & Auto Fit.", change to a specific residue

"File -> Save Coordinates", output pdb file

"File -> Export Map", output map file