Open ccp4/ccp4i and create new project
Click "Change Project", then "Add/edit project"
name "exp_6568" and choose the user directory **note: this is an example experiment number. You will use whatever number Crysalis Pro uses for your experiment
Scale intensities from data
Click menu in upper left corner, choose "Data Reduction and Analysis"
Click "Scale and Merge Intensities"
Job title: "scala"
Run "Ctruncate" to output Wilson plot and SFs after scaling; output single MTZ file
MTZ input "exp_6568.mtz" (from Crysalis Pro)
MTZ output: "exp_6568_scala1.mtz"
Under "Define Output Datasets", type Crystal "exp_6568" belonging to project "exp_6568" Dataset name "exp_6568"
Click "Run", then "Run Now"
Check quality of data by double-clicking on scala, then "Show Summary"
Multiplicity should be more than or equal to 3
R-merge should be less than 10%
Mean signal-to-noise ([I]/sd[I]) should be more than 10
Refine data
Click on menu in upper left corner, choose "Refinement"
Click "Run Refmac5"
Job title: "refmac-rigidbody"
Do "rigid body refinement" using "no prior phase info"
MTZ input: "exp_6568_scala1.mtz"
MTZ output: "exp_6568_refmac1.mtz"
PDB input: "1JJ0_apo.pdb" **note: this is an example pdb file. 1JJ0 is lysozyme with sucrose bound in the active site, apo means without water**
PDB output: "1JJ0_apo_refmac1.pdb"
Under "Refinement Parameters", Set resolution range from minimum [blank] to 3.00" (so, just set to 3 angstroms)
Also, make sure "Exclude data with freeR label..." is unchecked. Otherwise, an error will occur.
Run Now
Double-click on job, show log graphs, look at R-factor analysis, stats vs. cycle
Want this to be under 50% at this point
Click "Run Refmac5"
Job title: "refmac-restrained"
Do "restrained refinement" using "no prior phase information"
MTZ input: "exp_6568_scala1.mtz"
MTZ output: "exp_6568_refmac2.mtz"
PDB input: "1JJ0_apo_refmac1.pdb"
PDB output: "1JJ0_apo_refmac2.pdb"
Set resolution range from minimum [blank] to 2.00"
Run Now
Written up by John Y. Lee, June 2014