Merge pull request #407 from ExcitedStates/404-qfit_residue-is-missing

404 qfit residue is missing

example/README.md

@@ -4,11 +4,11 @@ Some of the advanced and specialized options available in qFit are demonstrated
 
 ### 1. Modelling alternate conformers for a residue of interest
 
-`qfit_residue [COMPOSITE_OMIT_MAP_FILE] -l [LABELS] [PDB_FILE] [CHAIN,RESIDUE]`
+`qfit_protein [COMPOSITE_OMIT_MAP_FILE] -l [LABELS] [PDB_FILE] --residue [CHAIN,RESIDUE]`
 
 Using the example 3K0N:
 
-`qfit_residue qfit_residue_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_residue_example/3k0n_refine.pdb A,113`
+`qfit_protein qfit_protein_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_protein_example/3k0n_refine.pdb --residue A,113`
 
 This will produce a parsimonious model containing up to 5 alternate conformers
 for residue 113 of chain A of 3K0N.
@@ -43,7 +43,7 @@ of the [Phenix software suite](https://phenix-online.org/).
 
 ### 4. Deactivate backbone sampling and bond angle sampling to model alternate conformers for a single residue of interest (faster, less precise)
 
-In its default mode, *qfit_residue* and *qfit_protein* samples backbone conformations
+In its default mode, *qfit_protein* samples backbone conformations
 using our KGS routine. This can be disabled using the *--no-backbone* flag.
 
 For even faster (and less precise) results, one can also disable the sampling of
@@ -58,20 +58,13 @@ the cost of precision:
 
 Using the example 3K0N:
 
-`qfit_residue qfit_residue_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_residue_example/3k0n_refine.pdb A,113 --no-backbone --no-sample-angle -s 20 -rn 45 --no-threshold-selection`
+`qfit_protein qfit_protein_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_protein_example/3k0n_refine.pdb --residue A,113 --no-backbone --no-sample-angle -s 20 -rn 45 --no-threshold-selection`
 
 For a full list of options, run:
 
-`qfit_residue -h`
+`qfit_protein -h`
 
-
-### 5. The same sampling parameters used in qfit_residue can be tweaked in qfit_protein:
-
-Using the example 3K0N:
-
-`qfit_protein qfit_protein_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_protein_example/3k0n_refine.pdb --no-backbone --no-sample-angle -s 20 -rn 45 --no-threshold-selection`
-
-### 6.  Parallelization:
+### 5.  Parallelization:
 
 The *qfit_protein* program can be executed in parallel and the number of concurrent processes
 can be adjusted using the *-p* flag.
@@ -81,7 +74,7 @@ Using the example 3K0N, spawning 30 parallel processes:
 `qfit_protein qfit_protein_example/3k0n_map.mtz -l 2FOFCWT,PH2FOFCWT qfit_protein_example/3k0n_refine.pdb -p 30`
 
 
-### 7. Modeling alternate conformers of a ligand
+### 6. Modeling alternate conformers of a ligand
 
 To model alternate conformers of ligands, the command line tool *qfit_ligand*
 should be used: