*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
My two cents and a summary:
1. omitting the atoms on a clearly indicated LYS residue is a choice.
It creates a striking phenotype and does not mislead. It might
however cause trouble in 'user' analysis software that will not like
LYS without its atoms. Plus, we know for sure that these atoms are
there, so we omit them ...
2. modeling the lys in a common rotamer is also a legitimate choice,
since B's will inflate. But, indeed thats not obvious when you look
at the structure. Also, most unfortunately most analysis software and
users will ignore B's.
3. putting occupancy to 0.0 does not look like a good choice to me.
the atoms still show on display and no user or software uses
occupancies any more than B factors, so to me it combines all the
trouble together. on top, some refinement programs when occ is 0,
they might switch off geometric restraints including VdW repulsion
and then its a real mess.
i still hesitate between 1 and 2, but my current choice is to use 2
(let B's inflate) and i admit i have limited sympathy for PDB users
that ignore B values and also cant be bothered to use the EDS (i.e. i
ignore the problem, which is not very nice, but ...)
Tassos
