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
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
phenix.fmodel:
http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fmodel.py
sftools (calc keyword): http://www.ccp4.ac.uk/html/sftools.html
diffraction image simulators from James Holton
mlfsom: http://bl831.als.lbl.gov/~jamesh/mlfsom/
nearBragg: http://bl831.als.lbl.gov/~jamesh/nearBragg/
fastBragg: http://bl831.als.lbl.gov/~jamesh/fastBragg/
many thanks for the replies.
Alastair
