[phenixbb] phenix.ready_set hydrogens not compatable with coot library
pafonine at lbl.gov
Mon Aug 23 09:03:28 PDT 2010
> This is absolutely true but, how about adding an option that would allow to (also) output a PDB version 2-formatted coordinate file at the end of a phenix.refine run? That way, one could read it directly into Coot for further model building, without hydrogens "exploding" at the first touch...
I guess (not entirely sure) that if you use a recent Coot version then
you shouldn't have problems with hydrogens. At least they don't fly away
at the first touch. I just tried myself.
Also, only a few gurus know about PDB format versions (2 or 3). Most of
people will get confused seeing two PDB files at the end of refinement
run, and they will flood us with questions about the differences between
these two files and why and so on ... So I would just stick to the
latest and wait a bit when the others adjust.
Actually, phenix.reduce can output v2 formatted PDB. I guess it is
"-OLDpdb" keyword. So if you really like to stick to the older format
> BTW, I think I already brought this up some time ago, but an option to output coordinate/map coefficients not only at the end of the refinement run, but also at the end of every intermediate macro cycle, would also be an useful addition to have.
I'm wondering why? Imagine you refine a huge model and do 20
macro-cycles... You will get a bunch of huge files...
Actually, if you run phenix.refine from the GUI, you can interactively
see how model and map changes during refinement. It's pretty cool.
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