Hi James, I guess it depends on what you put in your simulated Fobs. With phenix.fake_f_obs I can add lots of stuff including H, TLS, small random rigid-body shifts averaged over ensemble of MD simulated models, alternative conformations, libration motions of side chains around bonds, etc.. etc... (I forgot what else since I wrote this tool a while ago). With all these added I can't refine model back to R~0%, but get usual 10-20% depending on setup. I recall I was getting very realistic Fobs with corresponding refinement behaving the way I was expecting it to behave.
Pavel On Sat, Sep 7, 2013 at 4:54 AM, James Holton <jmhol...@lbl.gov> wrote: > I feel like I should point out that there is about a 20% difference > between "Fcalc" and something I would call a "simulated Fobs". Fcalc is > something that refinement programs compute many times every second as they > apply 100 years worth of brilliant ideas to make your model (Fcalc) match > your data (Fobs) as best we know how. Despite all this, one of the great > mysteries of macromolecular structure determination is just how awful the > "final" match is: R/Rfree in the 20%s or high teens at best. Small molecule > structures don't have this problem. In fact, they only recently started > depositing "Fobs" in to the CSD because for the most small molecule > structures "Fcalc" is more accurate than "Fobs" anyway. > > This has been hashed over on this BB a number of times, so I refer the > interested reader to the archives. But there are two major considerations > in turning a "pdb file" into a "simulated Fobs": > 1) the solvent > SFALL (part of the CCP4 suite) is a convenient tool for turning > coordinates into maps, or structure factors, but it doesn't "do" bulk > solvent unless you trick it. I wrote a jiffy for doing this here: > http://bl831.als.lbl.gov/~**jamesh/mlfsom/ano_sfall.com<http://bl831.als.lbl.gov/~jamesh/mlfsom/ano_sfall.com> > download the script, make it executable, and run it with no arguments to > see instructions for how to use it. What is fascinating about this very > crude bulk solvent implementation I did is that refinement programs with > much more sophisticated bulk solvent implementations have a heck of a time > trying to "match" it. If you want exactly the bulk solvent you would get > from phenix, use phenix.fmodel, but this will not be exactly the same as > the bulk solvent you get from REFMAC. Which one is right? Probably none of > them. > > 2) The R-factor Gap > One can try to simulate the R-factor gap (between Rmeas and Rfree) by > adding random numbers to "Fcalc" so that it becomes 20% different from > Fobs, but this is hardly a physically reasonable source of error. If you > do this enough times for the same PDB file and then "average over different > crystals" you'll still end up with a dataset that will refine to R/Rfree ~ > 0/0. > > This is the fundamental problem with making "simulated Fobs": we actually > have no good way of "modelling" whatever is causing this R-factor Gap, and > therefore no good way of simulating it. If we could simulate it, then some > refinement program would quickly implement a way to model the effect, and > give you R/Rfree of 0% again. There are about as many ideas for the cause > of the R-factor Gap as there are crystallographers out there, but to this > day nobody has come up with a "systematic error" that, when accounted for > in refinement, gives you a small-molecule-style R/Rfree for pretty much > anything in the PDB. Not even lysozyme. > > -James Holton > MAD Scientist > > > > On 9/5/2013 9:35 AM, Alastair Fyfe wrote: > >> Below are some links to tools for simulating Fobs data: >> >> phenix.fake_f_obs: http://cci.lbl.gov/cctbx_**sources/mmtbx/command_line/ >> **fake_f_obs.py<http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fake_f_obs.py> >> phenix.fmodel: http://cci.lbl.gov/cctbx_**sources/mmtbx/command_line/** >> fmodel.py <http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fmodel.py> >> sftools (calc keyword): >> http://www.ccp4.ac.uk/html/**sftools.html<http://www.ccp4.ac.uk/html/sftools.html> >> >> diffraction image simulators from James Holton >> mlfsom: >> http://bl831.als.lbl.gov/~**jamesh/mlfsom/<http://bl831.als.lbl.gov/~jamesh/mlfsom/> >> nearBragg: >> http://bl831.als.lbl.gov/~**jamesh/nearBragg/<http://bl831.als.lbl.gov/~jamesh/nearBragg/> >> fastBragg: >> http://bl831.als.lbl.gov/~**jamesh/fastBragg/<http://bl831.als.lbl.gov/~jamesh/fastBragg/> >> >> many thanks for the replies. >> Alastair >> >
