[phenixbb] A few questions

Pavel Afonine pafonine at lbl.gov
Wed Feb 6 09:25:25 PST 2008

Hi Christopher,

> In that case, then the occ of alt conf's tends to refine to greater than 1:
> ATOM    523 SE  AMSE A  32      23.654  11.792   6.216  0.56 14.04          Se
> ATOM    530 SE  BMSE A  32      23.570  12.284   6.796  0.46 13.91          Se

This should never happen and now I'm confused myself. To find out what 
is wrong, I need to reproduce it on my computer. Is it possible that you 
send me the data and model along with the exact command you used; I 
promise to keep it confidential. In this case I could have a closer look 
and tell exactly what's happening.

> And, if I use "group_occupancy" plus H's, then all the residues refined to an occ of 0.99!
> ATOM     30  N   ILE A   3      29.050  25.113   4.183  0.99  8.48           N

This is not surprising. As I wrote in my previous email in group 
occupancy refinement you refine one occupancy per group of atoms and 
this occupancy is not constrained, so it can refine to any value that 
the data suggests.


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