SampleDih

The SampleDih command allows to sample conformational space using internal coordinates. (Sampling in cartesian coordinates is done by Bert de Groot's CONCOORD plugin available under Linux by clicking on Edit > Sample > Object).

The dihedral angles to sample are indicated by selecting the two core atoms of the dihedral, i.e. the atoms at positions 2 and 3. In other words: all rotations around bonds between selected atoms will be sampled. If both atoms are fixed, the dihedral is automatically excluded from sampling.

The new dihedral angles assigned during the sampling process can be derived in three different ways:

Random - pick any random dihedral angle from -180 to 180 degrees.
Staggered - pick any dihedral angle in the energetically favorable staggered conformation.
Database - scan the PDB and extract 'knowledge-based' dihedral angles.

In the latter case, a non-redundant subset of the PDB is searched for stretches of scaffold residues that have a similar sequence and conformation as those in the starting structure. Conformational similarity is judged by calculating the RMSD over all those dihedral angles that have not been selected for sampling and remain frozen. Sequence similarity is judged by the BLOSUM62 matrix.

When searching conformational space during an energy-minimization protocol, it is often helpful to change only a small random subset of the selected dihedrals, so that good conformations can be kept. This is achieved by setting the Dihedrals parameter to a small number, e.g. '1' to change only one dihedral at a time.

The Structures parameter determines how many alternative conformations will be created as separate objects. Internally, all hits are ranked based on the structural and sequence similarity of the Scaffold residues, e.g. if 'Structures' is set to 10, the top 10 hits will be used. As a special case, setting 'Structures' to 1 tells YASARA to simply change the current conformation instead of creating additional objects. This is the method of choice for energy-minimization protocols, as it can also be done while a simulation is running.

Example 1:

Create 15 copies of the object containing Arg 50, where all side-chain dihedral angles of this residue are set to a random staggered conformation.

Example 2:

Create 10 copies of object 1crn, where all side-chains are set to typical conformations found by scanning the PDB for stretches of five scaffold residues with similar sequence and backbone structure. Minimize bumps.

Example 3:

Example 4:

Sample all dihedral angles in residues 709 to 711 using typical conformations found by scanning the PDB for stretches of seven (three selected + four scaffold) residues with similar sequence, where the outer four (two scaffold residues on either side) also have similar backbone structure. Create eight structures.

Example 5:

As above, but keep the side-chain conformations of residues 709-711 and use these conformations when scanning the PDB for stretches with similar structure. Assign the numbers of the created objects to 'objlist'.

# EXAMPLE SampleDih Ala # Requires YASARA Structure Clear LoadPDB 1crn Clean Style Ribbon,Stick # Turn all side-chains into CH3 groups (swap to Ala) SwapRes All,Ala # Sample the dihedral angle of rotation about the CA-CB bond randomly # This rotates the three hydrogens bound to the CB atom SampleDih CA CB,Method=Random,Structures=10,Dihedrals=999999,BumpSum=1 # Color the objects with a gradient, every object gets a different color ColorObj all,Blue,Cyan ColorAtom CA,Element ColorBG Red,Green,Blue,Magenta Pos Z=30 Ori 50,320,0

# EXAMPLE SampleDih Tyr # Requires YASARA Structure Clear LoadPDB 1crn Clean # SAMPLE THE POSSIBLE SIDE-CHAIN ROTAMERS OF RESIDUE TYR 29 BY SCANNING # THE PDB FOR STRETCHES OF 7 SCAFFOLD RESIDUES WITH SIMILAR STRUCTURE # AND SEQUENCE, AND TAKE THE DIHEDRAL ANGLES OF THE CENTRAL RESIDUE. SampleDih Sidechain CA Res Tyr 29,Method=Database,Structures=20,BumpSum=50,Scaffold=7 Style Ribbon ShowAtom Sidechain CA Res Tyr 29 Pos -5,1.5,15 Ori 80,37,-30

# EXAMPLE SampleDih Domain # Requires YASARA Structure Clear LoadPDB 1cfb DelRes !Protein Clean # SAMPLE THE POSSIBLE DOMAIN MOVEMENTS OF DROSOPHILA NEUROGLIAN. # ALL DEGREES OF FREEDOM ARE FROZEN, EXCEPT THE THREE LINKER # RESIDUES AND THE SIDE-CHAINS AT THE DOMAIN BOUNDARY. SampleDih Res 709-711 or Sidechain CA Res 655 681 739 740 796, Method=Database,Structures=7,BumpSum=5,Scaffold=4 Style Ribbon ColorRes 709-814,Blue,Cyan,Segments=Yes Pos -6,-4,90 Ori -61,42,-4

# EXAMPLE SampleDih Rotamers # Requires YASARA Structure Clear LoadPDB 1crn Style Ribbon,BallStick Clean best=999999. failures=0 # START SIMULATION FOR ENERGY CALCULATIONS ForceField Yamber2 Cutoff 7.86 Cell Auto,Extension=15 Sim On Sim Pause # REMEMBER THE BEST STRUCTURE SavePosAtom Obj 1,bestpos Console Off # REPEAT UNTIL PROCEDURE FAILED 30 TIMES while failures<30 # CHANGE A RANDOM SIDECHAIN ROTAMER SampleDih Sidechain CA Obj 1,Method=Database,Structures=1,Dihedrals=1,Bumpsum=0,Scaffold=5 # SHOW THE NEW ROTAMER ON SCREEN Wait 1 # CALCULATE ENERGY current=Energy if current<best # ACCEPT NEW STRUCTURE best=current SavePosAtom Obj 1,bestpos failures=0 else # REJECT NEW STRUCTURE, BACK TO BEST STRUCTURE LoadPosAtom Obj 1,bestpos failures=failures+1 ShowMessage 'Failures now (failures), best energy (0.00+best)..' # SHOW THE STARTING STRUCTURE DelObj SimCell LoadPDB 1crn SupAtom CA Obj 1,CA Obj 2 Ori 50,-35,0 Pos Z=20 Console On

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Sample dihedral angles

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