However, procheck ramachandran is deprecated these days as it is based
on older data than say molprobity. Obviously that won't matter just for
a list of phi/psi angles, but might affect selections e.g. what it
thinks are in a helix (cf Eleanor's message)
m
On Wed, 2009-01-14 at 14:39 -0500, Edward A. Berry wrote:
> 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
--
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