Sorry can't help it. The aggressive replies are mainly from senior PIs from US - friend in need is friend indeed.
On Thu, Apr 23, 2015 at 2:20 PM, Bernhard Rupp (Hofkristallrat a.D.) < hofkristall...@gmail.com> wrote: > 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 > > >
