Below are examples of large errors showing small discrepencies between calculation of dihedral angles after rotation in this code base and with the VMD software suite (https://www.ks.uiuc.edu/Research/vmd/) when rotations are large (~50 degrees). This error does not appear to show for smaller rotations (~4 degrees). Examples are shown below with logs and visualizations with VMD.
Input with error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 159 -o output.pdb -e pdb
Output log:
Command Line: ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 159 -o output.pdb -e pdb
Reading structure file: example_files/ILE_conect_110.pdb
Not printing covalent bond matrix
Number of dihedrals identified in structure: 4
Calculating initial dihedral angles.
Columns: Angle, Angle Type (phi, psi, etc), Residue Name, Residue Number, Dihedral Number
-86.610730 phi ILE 2 0
165.397344 psi ILE 2 1
99.733809 chi1 ILE 2 2
-71.905838 chi2 ILE 2 3
Done reading structure file: example_files/ILE_conect_110.pdb
Found dihedral number: 2
Changing dihedral angle chi1 in residue number 2 by 59.266191 degrees.
Rotation complete. Please check the accuracy of the operation.
User input angle: 159.000000
Angle after rotation: 159.000000
VMD dihedral:
Input without error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103 -o output.pdb -e pdb
Output log:
Command Line: ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103 -o output.pdb -e pdb
Reading structure file: example_files/ILE_conect_110.pdb
Not printing covalent bond matrix
Number of dihedrals identified in structure: 4
Calculating initial dihedral angles.
Columns: Angle, Angle Type (phi, psi, etc), Residue Name, Residue Number, Dihedral Number
-86.610730 phi ILE 2 0
165.397344 psi ILE 2 1
99.733809 chi1 ILE 2 2
-71.905838 chi2 ILE 2 3
Done reading structure file: example_files/ILE_conect_110.pdb
Found dihedral number: 2
Changing dihedral angle chi1 in residue number 2 by 3.266191 degrees.
Rotation complete. Please check the accuracy of the operation.
User input angle: 103.000000
Angle after rotation: 103.000000
Below are examples of large errors showing small discrepencies between calculation of dihedral angles after rotation in this code base and with the VMD software suite (https://www.ks.uiuc.edu/Research/vmd/) when rotations are large (~50 degrees). This error does not appear to show for smaller rotations (~4 degrees). Examples are shown below with logs and visualizations with VMD.
Input with error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 159 -o output.pdb -e pdbOutput log:
VMD dihedral:
Input without error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103 -o output.pdb -e pdbOutput log:
VMD dihedral: