Except that Procheck is now ages behind the standard, with Molprobity being the standard. I'm not sure even if Coot uses the latest libraries. Those I quoted in example below come from latest Molprobity (Phenix that is) and are the latest.
Pavel On Fri, Mar 24, 2017 at 2:55 PM, Edward A. Berry <ber...@upstate.edu> wrote: > On 03/23/2017 11:39 PM, Alex Lee 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. >> >> Well, you can always AWK out 3 residues and run procheck on them, > something like: > > awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb > procheck w.pdb 1.8 > followed by: > gs w_01.ps > or: > ps2pdf w_01.ps > acroread !$ > > (The AWK command will have to be tweaked if fields run together in the > pdb due to large numbers or alt. conformations for these three residues) > > I agree such a feature would be useful in coot. Sometimes you want to > know if an outlier is just outside or way outside, or if it is halfway > between two allowed regions, and with large, low-quality structures it is > hard to find the residue in the crowded rama plot. > Clickable points in the R plot fills the bill going one way, now > highlighting > points corresponding to selected residue would be the other half. > eab >
