> Pavel’s statement is likely a bit of an exaggeration, but he has a valid > (yet hard to prove point). The default in CCP4i was (and is?) to use > hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default is indeed to use H atoms only if present in input, whereas the current documentation (http://www.ccp4.ac.uk/html/refmac5/keywords/restraints.html#makecif) says (quoting verbatim): HYDR [ Yes | No | All ] (Default HYDRogens All) How to deal with the hydrogen atoms. Y - if hydrogens are present in the input file, use them, N - ignore hydrogens even if they are present in the input coordinate file, A - add all hydrogens in their riding positions and use them for geometry and structure factor calculations. They also contribute to the gradient and second derivative matrix of geometry residual. The documentation in this case also corresponds to the source code default: MAKE_HFLAG = 'A' Which do we believe: GUI or source code? Personally I'm much more inclined to trust the defaults in the code over either the documentation or the GUI, because I have a strong suspicion that the CCP4i defaults (and yes even on occasions the documentation!) lag somewhat behind the "community view" on this as represented by the current code version. Or is this an incorrect perception? > Because there were some reporting errors in the past > (http://proteincrystallography.org/ccp4bb/message18808.html) it is hard to > tell from the PDB when refinement with hydrogens became hip. Discussions on > this BB show that at the use of riding hydrogens is still not fully > accepted, especially at low resolution (where they actually help most). Documentation says: "For low resolution and early stages it is better to use MAKE HYDR N, i.e. do not use hydrogens even if they are present in the input file.". Cheers -- Ian
