John Pak wrote:
Hi, sorry if this was posted earlier. How can I calculate a
Ramachandran plot, but output the information to a text file list?
i.e. something like Ala51, phi=X, psi=Y.
I can't seem to find this information in the ccp4 SFCheck/Procheck log
file.
And lets not forget procheck, since its included with ccp4 and you
probably already have it. After you run procheck on your protein
(procheck pdbname.pdb 1.8), there is a text file pdbname.rin
which lists phi, psi, omega and sidechain dihedrals for each residue:
phi psi omega chi1 chi2 chi3 chi4
14ASN A 15 E -89.06 141.45-179.73 -63.59 -55.39 999.90 999.90 -2.14 0.00
34.00 89.18 88.838 88.830 8 45 1.980 0.762
15VAL A 16 E-139.67 138.33 177.89-170.03 999.90 999.90 999.90 0.00 0.00
36.23 87.91 86.643 87.253 8 50 0.147 0.499
16THR A 17 E-144.59 139.86-179.12 51.94 999.90 999.90 999.90 -2.64 0.00
34.56 84.27 86.238 85.020 8 40 0.421 0.536
You also have a .ps file pdbname_01.ps with the graphical ramachandran
which you can view with gv or gs, or convert to pdf with ps2pdf
DSSP also list phi-psi angles, in two columns far to the right.
Ed
