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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 ...
When an end-user sees missing atoms, he/she might at least smell a rat.
I have met non-xtallo scientists who were misled because they were
unaware of B's and occu, and took the coordinates at their face value!
So, this seems to be an approach that is least likely to mislead the user.
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.
I have such residues is my previous structures! But I am also not sure
how many non-xtallo end-users analyze atomic coordinates in the context
of B's. A good proportion of non-xtallo folks perhaps download the
coordinates and stare at it in a display program. If they see what they
want, I am not sure most of the time they open up the PDB file and then
figure out what the different columns mean.
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 agree. This does not seem to be a good approach to me since I have met
non-xtallo end-users one time that were misled by ~ 20 residues in a
structure with occu=0. They downloaded the structure with no knowledge
of the world of B's and occupancies. They made a model and hypothesis
for potential biological interactions based those 20 residues with ZERO
occupancies in their conference poster, the reported atomic coordinates
of which (in the PDB file) being pure fantasy in that particular
structure (since we pursued work on the same complex).
Why not be cautious and assume that the non-xtallo end user will NOT
open up the PDB file and look at B's, occupancies and then try to use
that to interpret the structure? If they do, then that's a bonus. If
they don't, we at least make certain we minimize the likelihood for
misinterpretation. This would be a good courtesy to extend to the
biological community.
Raji
--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
