Just create a new tag, say _atom_site.imaginary_site, which is either
true or false for every atom. Then everyone would be able to either
filter out the fake atoms or leave them in, without ambiguity or
confusion.
Aside from being a binary rather than continuous parameter, how exactly
does
Dear young (and not so young) impressionable friends of Dark Matter,
Thank you for all the kind requests for my PRL paper [1]. Unfortunately, I have
to retract the paper, but buying me a beer next time we meet might help me to
forget you ever asked for it.
One (!) respondent got it right
On Apr 1, 2011, at 4:00 PM, Ed Pozharski wrote:
I need to calculate the electron density values for a list of spatial
locations (e.g. atom positions in a model) using an mtz-file that
already contains map coefficients. To write my own code may be easier
than I think (if one can manipulate mtz
I guess I missed it in the flurry of replies to this thread over the
last few days, but what exactly is so terrible about keeping the atoms
(since you have chemical evidence from protein sequence that they are
there, and even if there is X-ray damage they were originally there and
are likely
Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.
But nobody knows what other software is out there being used by
individuals or small groups. And the more remote the authors
of that
I think Frances is right, i.e. most non crystallographers ignore
anything beyond the x, y, z coordinates (i.e. beyond column 54)
[as Frances wrote].
Thus if a crystallographer put in coords that he/she does NOT see,
even with OCC=0, or an enormously large Bfactor, these coords are usually
