Hi Ethan,
yes, you are absolutely right, you would need to define somehow where
your model is... But you could, at least hypothetically, use non-atomic
models for this! Like cylinders (*), spheres and similar shapes. This is
what the density looks like at those "super-low" resolutions.
(*)
BOROVIKOV, B. A., VAINSTEIN, B. K., GELFAND, I. M. & KALININ, D. I.
(1979). Kristallografiya, 24, 227-238.
KALININ, D. I. (1980). Kristallografiya, 25, 535-544.
V. Yu. Lunin, A. G. Urzhumtsev, E. A. Vernoslova, Yu. N. Chirgadze, N.
A. Neveskaya and N. P. Fomenkova. Acta Cryst. (1985). A41, 166-171.
Anyway, looks like we are about to diverge from the original subject so
I stop rambling -:)
All the best!
Pavel.
On 9/14/10 1:10 PM, Ethan Merritt wrote:
On Tuesday 14 September 2010 12:44:37 pm Pavel Afonine wrote:
Hi Ethan,
I do not favor depositing riding hydrogen coordinates for
the same reason that I do not like the recent PDB preference
for depositing ANISOU records for structures that have been
refined with TLS.
In both cases the enumeration of these many thousands of
parameter values gives the strong, but false, impression that
they have been individually modeled. They have not.
following this logic one could say that the individual x,y,z coordinates
listed in ATOM records for a structure refined at very low resolution
using rigid-body refinement only (or torsion angle Simulated Annealing
only) also may make a false impression that these coordinates were
refined individually.
I agree with this, at least for the case of true rigid-body.
But you would still need to describe somehow the coordinates of all the
atoms in your rigid model. If it came straight out of the PDB, then
in principle it would suffice to give the PDB+CHAIN code and the
rotation/translate matrix. But if any adjustments were made, which
is I think typical if only to correct for sequence differences,then as a
practical matter you still need to provide the true starting coordinates.
And at that point you might as well provide the ending coordinates instead,
since it's the same amount of information.
Ethan
