Thanks Pavel, is there a command that can tell secondary structure assignment based on Rama plot of each residue beside phi and psi? for example : A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix
On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine <pafon...@gmail.com> wrote: > Trivial using command line. Example: > > - get a file from PDB: > > phenix.fetch_pdb 1yjp > > - get all phi/psi for all residues: > > phenix.ramalyze 1yjp.pdb > residue:score%:phi:psi:evaluation:type > A 2 ASN:56.93:-60.58:141.19:Favored:General > A 3 ASN:48.44:-119.25:125.15:Favored:General > A 4 GLN:16.23:-126.16:112.81:Favored:General > A 5 GLN:55.13:-114.98:126.76:Favored:General > A 6 ASN:6.17:-116.42:97.69:Favored:General > SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A where > applicable) > SUMMARY: 0.00% outliers (Goal: < 0.2%) > SUMMARY: 100.00% favored (Goal: > 98%) > > Pavel > > > On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty <nwmoria...@lbl.gov> > wrote: > >> Alex >> >> It seems that nobody has answered your question. I'm not sure what you >> can do in CCP4, but if I understand your question correctly, you can >> perform a comprehensive validation in Phenix complete with Ramachandran >> plot including clickable points relating to your residues which allow you >> to see the residues in Coot. >> >> Happen to help further on the PHENIXBB or off-line. >> >> Cheers >> >> Nigel >> >> --- >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov >> Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov >> >> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee <alexlee198...@gmail.com> >> wrote: >> >>> Dear All, >>> >>> Is there a tool or software which can give Ramachandran information of >>> individual residues in a plot? >>> >>> I used Coot to check for Ramachandran plots, but it shows all the >>> residues in a coordinate I put in Coot, not individual one. I also use >>> "residue info" in coot, it tells Ramachandran "phi psi" angles of >>> individual residue, but it does not show it in a plot, only numbers. >>> >>> Thanks ahead for any input. >>> >>> >> >
