May be not exactly what you want, but should be close: phenix.secondary_structure_restraints 1yjp.pdb
then here you have options - for output format: format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage - for search (annotation method): search_method = *ksdssp mmtbx_dssp from_ca cablam I suggest you please with them and see which one suits you most. Pavel On Fri, Mar 24, 2017 at 1:18 PM, Xiao Lei <xiaolei...@gmail.com> wrote: > 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. >>>> >>>> >>> >> >
