Well, with full respect to your sensitivities as far as your own person is concerned: if you play rough (and 5 exclamation marks qualify by commonly accepted email etiquette as incipient flame, at least), you need to be willing to take a few as well...
Best, BR ----------------------------------------- Trigger warning --------------------------------------------------- This message may or may not contain references to issues of privilege and oppression in- cluding but not limited to enantiophobia, point classism, heteroatomism, transbondism, cisbonding, sizeism, curvature, references to color, alcohol, blood, small insects, cancer cells, and any combination thereof that may cause symptoms ranging from discomfort and anxiety to violent physical response in sensitive individuals and must therefore be labeled as potentially hazardous to your comfort and well-being. ----------------------------------------- Trigger warning --------------------------------------------------- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Misbah ud Din Ahmad Sent: Thursday, April 23, 2015 2:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! I feel rather uncomfortable and cornered with the aggressive replies and phrases like "throwing stones", "public humiliation" etc., which suggest that I have some personal enmity with the author. The structure is in the public domain and questions can be asked about it. I as a beginner in crystallography learn from each discussion on this board and such harsh and insinuating responses may, in future, deter people like me from posting any questions at all and learning refinement strategies like the one which Pavel outlined to improve such type of structures. Best Misbha On Thu, Apr 23, 2015 at 9:17 PM, Gert Vriend <gerrit.vri...@radboudumc.nl> wrote: At around 4.0 A resolution one normally cannot talk about accuracy. The density will at most locations not warrant any detailed interpretation. If, at 4.0 A resolution, you move atoms around a bit, you will not see significant changes in R/Rfree. So, you can do whatever you want, more or less. If the refinement puts great emphasis on the secondary structure (i.e. tries to force the Ramachandran plot, then you get a good Ramachandran plot, but if they put more weight of the fit to the density, you get a slightly lower R (and perhaps even Rfree) at the cost of the Ramachandran plot. And all of that is meaningless. At this resolution you have to check if the fold is likely to be correct. I superposed just any high(er) resolution domain with high sequence similarity at the corresponding 3bdn domain, and I take any bet that the fold of 3bdn is right (at least of the domain I looked at, and I extrapolate to the other domain). PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/) cannot improve this one, and WHAT_CHECK (http://swift.cmbi.ru.nl/gv/pdbreport/) throws its hands up in the air. At 4.0 A you should be happy with an indication of the fold (and with the fact that the authors probably went through great pains for you getting these coordinates close to where they should be). Gert
