Greetings, everyone. I got the pdb file of an enzyme, but I don't know how to write the constraints of its active sites.
Could anyone help me solve this problem?
Much appreciate it.
When I open the pdb file with txteditor, I can see coordinates as:
ATOM 1 N HIS A 27 10.218 -30.379 -16.292 1.00 12.31 N
ATOM 2 CA HIS A 27 10.486 -29.045 -15.829 1.00 12.44 C
ATOM 3 C HIS A 27 11.803 -28.537 -16.417 1.00 12.46 C
ATOM 4 O HIS A 27 11.912 -27.351 -16.894 1.00 11.54 O
ATOM 5 CB HIS A 27 10.509 -29.082 -14.280 1.00 10.82 C
ATOM 6 CG HIS A 27 10.402 -27.733 -13.630 1.00 11.50 C
ATOM 7 CD2 HIS A 27 10.266 -26.472 -14.145 1.00 12.66 C
ATOM 8 ND1 HIS A 27 10.504 -27.583 -12.255 1.00 13.07 N
ATOM 9 CE1 HIS A 27 10.391 -26.290 -11.951 1.00 14.54 C
ATOM 10 NE2 HIS A 27 10.244 -25.612 -13.074 1.00 11.43 N
TER 11 HIS A 27
ATOM 12 N HIS A 82 15.205 -20.416 -13.135 1.00 12.48 N
ATOM 13 CA HIS A 82 15.416 -21.885 -13.107 1.00 13.11 C
ATOM 14 C HIS A 82 16.910 -22.184 -12.930 1.00 12.05 C
ATOM 15 O HIS A 82 17.251 -23.177 -12.288 1.00 13.17 O
ATOM 16 CB HIS A 82 14.874 -22.584 -14.379 1.00 13.33 C
ATOM 17 CG HIS A 82 13.390 -22.639 -14.405 1.00 12.06 C
ATOM 18 CD2 HIS A 82 12.512 -23.596 -14.011 1.00 12.97 C
ATOM 19 ND1 HIS A 82 12.649 -21.563 -14.827 1.00 10.57 N
ATOM 20 CE1 HIS A 82 11.356 -21.860 -14.688 1.00 14.15 C
ATOM 21 NE2 HIS A 82 11.257 -23.079 -14.182 1.00 13.12 N
TER 22 HIS A 82
How can I determine the distance, angles and dihedrals between the two residues?
Hi Albert !
I use pymol for calculating the distance, angles and dihedrals between the two residues.
To know more about constraints go to https://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/fil...
That's just what I've been looking for. Thank you very much!
Hi Albert,
In addition, if you know python, you can look into using PyRosetta and the iPython shell to do it in code.