I guess, most hydrophilic side chains on the surface are flexible, they
don't keep the same conformation. If you cut those side chains off, the
surface will be looking pretty hydrophobic and misleading (and very
horrible). I prefer to see them intact. I know, most of them are
flexible and don't have one exact position, but it's OK. I know they are
there not far from the main chain. Usually, their exact position is
irrelevant.
Maia
Jacob Keller wrote:
Well, what about getting the default settings on the major molecular
viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
While the b cutoff is still be tricky, I assume we could eventually
come to consensus on some reasonable cutoff (2 sigma from the mean?),
and then this approach would allow each free-spirited crystallographer
to keep his own preferred method of dealing with these troublesome
sidechains and nary a novice would be led astray....
JPK
On Sun, Apr 3, 2011 at 2:58 PM, Eric Bennett <er...@pobox.com> wrote:
Most non-structural users are familiar with the sequence of the proteins they
are studying, and most software does at least display residue identity if you
select an atom in a residue, so usually it is not necessary to do any cross
checking besides selecting an atom in the residue and seeing what its residue
name is. The chance of somebody misinterpreting a truncated Lys as Ala is, in
my experience, much much lower than the chance they will trust the xyz
coordinates of atoms with zero occupancy or high B factors.
What worries me the most is somebody designing a whole biological experiment around an
over-interpretation of details that are implied by xyz coordinates of atoms, even if
those atoms were not resolved in the maps. When this sort of error occurs it is a level
of pain and wasted effort that makes the "pain" associated with having to build
back in missing side chains look completely trivial.
As long as the PDB file format is the way users get structural data, there is really no
good way to communicate "atom exists with no reliable coordinates" to the user,
given the diversity of software packages out there for reading PDB files and the
historical lack of any standard way of dealing with this issue. Even if the file format
is hacked there is no way to force all the existing software out there to understand the
hack. A file format that isn't designed with this sort of feature from day one is not
going to be fixable as a practical matter after so much legacy code has accumulated.
-Eric
On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote:
To the delete-the-atom-nik's: do you propose deleting the whole
residue or just the side chain? I can understand deleting the whole
residue, but deleting only the side chain seems to me to be placing a
stumbling block also, and even possibly confusing for an experienced
crystallographer: the .pdb says "lys" but it looks like an ala? Which
is it? I could imagine a lot of frustration-hours arising from this
practice, with people cross-checking sequences, looking in the methods
sections for mutations...
JPK
