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PdbStat commands for some useful tasks

 

Fixing label of atoms

 

1.     read coo pdb 2jqn.pdb                  # will read coords for 2jqn.pdb file

2.     all                                                      # all models

3.     fix stereo                                          # will locate right IUPAC labels for prochiral atoms

4.     to iupac                                            # the same as 3

 

 

Well defined ranges using dihedral angle order parameter (DAOP) and superposition

 

1.     read coo pdb 2jqn.pdb                  # will read coords for 2jqn.pdb file

2.     all                                                       # all models

3.     order 1.8                                           # S(phi) + S(psi) >= 1.8, as output: residue ranges

4.     rmsd best backbone                       # optimal rotation, calc of RMSD for backbone atoms in ranges

5.     enter                                                  # to let the program do the calculation and write a file

 

 

Finding the "core" atoms (ranges) for a structure

 

1.     read coo pdb 2jqn.pdb                   # read coords from 2jqn.pdb file

2.     all                                                        # all models

3.     find -bb                                             # Finds the core atoms using all backbone atoms

 

 

Well defined ranges (using expansion of FindCore core, NOTE: only if version >= 5.9 )

In this example the command "expan -bb core" will first run find - bb to locate the core atoms and then a "expansion" of that core is performed outputting the final ranges.

 

1.     read coo pdb 2jqn.pdb                   # read coords from 2jqn.pdb

2.     all                                                        # all models

3.     expan -bb core                                 # perform FindCore and then expands the core

4.     write coo pdb FileName                 # write the coords in PDB format

 

 

NOE completeness ( NOTE: only if version >= 5.9 )

In the next example we will read some PDB coordinates, some restraints and issue the commands to calculate the NOE completeness (default values) for a set of expected NOEs built from sequence data.

 

1.     read coo pdb 2jqn.pdb                  # loads coordinates from 2jqn.pdb

2.     all                                                       # all models

3.     read cons cns 2jqn.mr                    # loads restraints (CNS format)                        

4.     noe comple                                       # NOE completeness using sequence to build the set of expected NOEs

 

The same as before but building the set of expected NOEs from the chemical shift list

 

1.     read coo pdb                                   # loads coordinates from

2.     all                                                       # all models

3.     read cons cns                                   # loads restraints (CNS format)

4.     read shift                                          # loads shifts from (any BMRB 2.x, 3.x)

5.     noe comple shift                             # Completeness using the shifts to build expected set of NOEs

 

 

Restraints analysis

 

1.     read coo pdb 2jqn.pdb                  # loads coordinates from 2jqn.pdb

2.     all                                                       # all models

3.     read cons cns 2jqn.mr                    # loads restraints stored in CNS/Xplor format in 2jqn.mr

4.     to iupac                                             # fix labels

5.     noe to iupac                                     # convert internally to match coords

6.     noe ana                                             # analyse the set of restraints loaded

7.     see viol sum                                     # NOE ,ACO violation analysis using summ average

 

 

RDC

In this case the file with constraints has also RDC data that is read by PdbStat and then Da and R (axial and rhombic) are determined with expression of Q and RMS for each model in turn.

 

1.     read coo pdb                                  # loads coordinates from

2.     all                                                      # all models

3.     read cons cns                                  # loads restraints from

4.     eval dar                                             # RDC analysis, will calculate Da and R giving results for Q, RMS

Writing constraints to different formats

 

1.     read coo pdb 2jqn. pdb                 # loads coordinates from 2jqn.pdb

2.     read cons cns 2jqn.mr                   # loads restraints from 2jqn.mr

3.     to iupac                                            # fix stereo and shift to IUPAC lables

4.     noe to iupac                                     # convert atom labels in NOE to match IUPAC

5.     write noe rosetta File                    # write file File with NOE restraints in Rosetta 3.x format

6.     write aco rosetta File                      # write ACO (Dihedral restraints) in Rosetta 3.x format