Hi Ed,
I didn't really open a can of worms... Sorry if I did!
But there are many things affecting R-factors not
being reported. Do I have to deposit the bulk solvent mask?
Not that many and most of them are reported (at least those that may
affect the R-factor "significantly"). The model structure factor is
(well different programs may define it differently, but they normally
report the corresponding parameters) (as used in phenix.refine):
Fmodel = scale_overall * exp(-h*U_overall*ht) * (Fcalc + k_sol *
exp(-B_sol*s^2/4) * Fmask)
- anisotropic scale matrix (U_overall) is reported as "REMARK 3 B11
:", ...;
- ATOM and ANISOU is enough to calculate Fcalc (the difference between
scattering tables used: it1992, wk1995 or n_gaussian will not make
visible difference) (the difference in algorithm FFT vs DIRECT used to
compute Fcalc will not, normally, make difference too);
- Bulk solvent k_sol and B_sol are reported: "REMARK 3 K_SOL" or
similar;
- Reproducing Fmask you at least need "grid_step", "solvent radius" and
"shrink truncation radius", which phenix.refine reports all:
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.347
REMARK 3 B_SOL : 29.392
So I think you have all (or most of) you need to reproduce the R-factor
statistics IF PDB FILE IS COMPLETE.
I think
the fundamental question is why do you need to be able to reproduce the
exact R-factors. Perhaps depositing FC and PHIC along with FP and SIGFP
will solve your problem?
Given so little information and effort to do so, I don't see why not?
It's just a simple formula that relies on a number of simple parameters
that are easy to report and in fact they are reported in PDB file in
most of cases. If you have a few atoms model, you could use a pen and
calculator to do so -:) It's a great and simplest validation tool: if
you unable to reproduce the R-factors then something is wrong with the
1) file, 2) structure or 3) your software. However, if you explicitly
allow the R-factors to be not ("exactly") reproducible, then you
immediately loose the way to address "1)-3)".
Don't get me wrong - I think it's important that deposited structures
provide complete information about the model. But why are riding
hydrogens so particularly important when reporting crystallization
conditions is not mandatory? Or bulk solvent parameters? Or geometry
restraints you used for the custom ligand (thus it's not in the standard
libraries)?
Absolutely agree! So, let's make a tiny step forward and keep whatever
we can easily keep, and hope that in future more information will be
preserved (such as complete foot-print of restraints used and so on).
I did a quick (and dirty) survey of the PDB and found that less than 2%
of structures report hydrogens.
Well, years back people used to cut low resolution data at 5...8A until
it became clear that it's a not so good idea. Nowadays, I don't think
anyone will throw away low resolution data. Similar rationale with
hydrogens. Let's follow the progress and not look back (telling myself) -:)
All the best!
Pavel.
