Hi,
> Any time you do a thought experiment you make a fake-data data set, the > "true" phases and "true" amplitudes become the ones you put into the > simulation process. This is by definition. Is there potential for > circular reasoning? Of course! But you can do controls: > this is so much true! This is what I've been doing for development and testing all the time since started working for Phenix! Fully controlled thought/numerical experiments done this way are super-helpful (but obviously have limitations!). > If you start with an ordinary single-conformer coordinate model and > flat bulk solvent from refmac to make your Ftrue, then what you will > find is that even after adding all plausible experimental errors to the > data the final Rwork/Rfree invariably drop to small-molecule levels of > 3-4%. This is true even if you prune the structure back, shake it, and > rebuild it in various ways. The difference features always guide you > back to Rwork/Rfree = 3/4%. However, if you refine with phenix.refine, > you will find Rwork/Rfree stall at around 10-11%. This is because Ftrue > came from refmac and refmac and phenix.refine have somewhat different > bulk solvent models. If Ftrue comes from phenix and you refine with > refmac you get similar "high" R values. High for a small molecule > anyway. And, of course, if you get Ftrue from phenix and refine with > phenix you also get final Rwork/Rfree = 3/4%. If you do more things that > automated building doesn't do, like multi-headed side chains, or get the > bulk solvent from an MD simulation, then you can get "realistic" > Rwork/Rfree in the 20%s. All of this is the main conclusion from this > paper: https://dx.doi.org/10.1111/febs.12922 Even within Phenix alone this is true if you switch between different scaling/bulk-solvent models or play with automation levels (such as ignoring reflection otliers, etc). Pavel ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
