[phenixbb] Rant: B vs TLS, anisou, and PDB headers
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Sat Mar 29 10:35:33 PDT 2008
Just spent an hour trawling docs, BBs (recent threads) and logs to
figure out what the hell my B column is telling me (phenix vs refmac vs
Oh dear, it's a disaster area, quite Heissenbergian... the most
important number (uncertainty) is itself unknowable:
* Phenix writes total ADP, Refmac writes residual ADP.
* Refmac writes a remark -- pdbdep strips it (!?!!?)
* Phenix writes no remark (I think?)
* Refmac writes different numbers to TLSOUT and pdb header (trace of S)
* Phenix duplicates the information in header (TLS) and ANISOU cards,
the latter thereby making implicit what should be explicitly stored:
how the ADPs are connected.
* Refmac, given phenix TLS-originating ANISOUs, flattens them into first
number, but does not remove them
* PDB does not care
I'd like to appeal for an urgent consensus -- which should be unusually
easy, since it involves only two programs and one repository.
My strong recommendation, from first principles of usability: residual
B into ATOM, no TLS in ANISOU, and the rest into the header. I know
it's religious, but here's the reasoning:
==> the end-user looks *locally*, that's what ATOM and ANISOU are for.
==> global stuff (cell, symmetry, NCS, and yes, TLS) belongs in the
header -- as do what's still missing, namely twinning, lattice
modulations, scatter factors, and restraints.
Yes, we crystallographers want easy B-factor stats (phenix's reason),
but then lets fix the analysis programs to look at the header as well.
And yes, packing and internal motions (TLS) are all very important for
analysis - but that is why it should be explicit in the header, so that
graphics tools have easy access to it.
End rant (but not end hope :)
More information about the phenixbb