[phenixbb] rotamers

Ed Pozharski epozh001 at umaryland.edu
Wed Mar 23 17:24:18 PDT 2011

On Wed, 2011-03-23 at 14:39 -0700, Pavel Afonine wrote:
> Some people tend to chop them off (which I do not not not like), some 
> let the refinement programs do what they want, and the programs
> stupidly 
> tends to stick these sidechains in whatever density is available
> around 
> (this is bad too).

Yes, there are basically three options:

1) cut the side chain down to whatever is still visible in the density 
2) let the refinement proceed as is
3) set side chain atom occupancies to zero

Personally, I have evolved from 2) to 1).  The argument was that
omitting atoms will confuse some end users, and refinement will
essentially take care of it by increasing the B-factors.  I have seen
some quite convincing evidence since that the disordered side chains do
have a detectable effect on the rest of the model, and thus leaving them
in makes a model worse.  Other half of the argument was of semantic
nature and referred more to replacing disordered residues with alanines,
which is silly because we know from sequence it's not alanine and we
know the atoms must be in the vicinity.  But on the other hand we
exclude whole segments of sequence sometimes, such as disordered loops
and termini, so why not side chains?  Missing atoms are just that -
missing from the density.  Chemically it is still a lysine, according to
the residue name.

The third option (the one you gravitate towards) seems problematic to me
for the following reasons.  The meaning of the occupancy is that the
atom distribution in space is multimodal, and it spends certain fraction
of time vibrating around the specified position.  So what is the meaning
of zero occupancy?  This is the average atomic position, but it spends
zero time here?  Makes no physical sense, and in fact is wrong since
there is some non-zero probability that the disordered side chain will
occupy the designated conformation.  Of course, structural model may be
considered a *mathematical* model, and it does not have to be strictly
interpretable (or interpretable the way I see most logical, anyway).

As for end-user argument, I would say that omitted atoms are better than
high B-factors or zero occupancies, as it is more likely to attract
attention to the fact that side chain conformation is undefined (coot,
however, does highlight zero occupancy atoms).  It is true though that
the "end-user argument" is inherently weak, since nobody can be held
responsible for self-inflicted damage due to lack of knowledge.  Except
MacDonalds and microwave oven manufacturers, of course. 

Hurry up, before we all come back to our senses!
                          Julian, King of Lemurs

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