On Sunday, April 03, 2011, Jacob Keller wrote:
> To the delete-the-atom-nik's: do you propose deleting the whole
> residue or just the side chain?
Omit the atoms beyond CB for which there is no apparent density.
Always place CB if the backbone trace is reasonable, because its
location is fixed a priori by known stereochemistry.
As a practical matter, I use Coot's "stub" command.
Ethan
> 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
>
> On Sun, Apr 3, 2011 at 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.)
> <hofkristall...@gmail.com> wrote:
> > Thus my feeling is that if one does NOT see the coords in the electron
> >
> > density, they should NOT be included, and let someone else try to model
> >
> > them in, but they should be aware that they are modeling them.
> >
> > Joel L. Sussman
> >
> >
> >
> > Concur. BMC p 680 ‘How to handle missing parts’
> >
> >
> >
> > Best wishes, BR
> >
> >
> >
> > On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:
> >
> >
> >
> > 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 software are from protein structure solution the more
> > likely it is that they have not/will not properly handle atoms
> > with zero occupancy or high B values, for example.
> >
> > I am absolutely positive that there is software that does its
> > voodoo on ATOM/HETATM records and pays absolutely no attention
> > to anything beyond the x, y, z coordinates (i.e. beyond column 54).
> >
> > Frances Bernstein
> >
> > =====================================================
> > **** Bernstein + Sons
> > * * Information Systems Consultants
> > **** 5 Brewster Lane, Bellport, NY 11713-2803
> > * * ***
> > **** * Frances C. Bernstein
> > * *** f...@bernstein-plus-sons.com
> > *** *
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> > =====================================================
> >
> > On Sat, 2 Apr 2011, Jacob Keller wrote:
> >
> > 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 still there in a subset of the molecules), but changing
> >
> > occupancy to zero as an acknowledgment that your data does not provide
> >
> > evidence to support a specific atomic position for these atoms?
> >
> >
> >
> > Some users might pull up the structure, see those atoms, and think
> >
> > their positions were based on data, which they were not, and then draw
> >
> > conclusions based on them. I agree that occ=0 is tantamount to the
> >
> > suggestion you queried, however.
> >
> >
> >
> > A somewhat key question might be: across the various molecular
> >
> > visualization programs, what is the default way to handle atoms with
> >
> > occ=0? Perhaps those programs might be the best place to fix the
> >
> > problem...
> >
> >
> >
> > JPK
> >
> >
> >
> >
> >
> > *******************************************
> >
> > Jacob Pearson Keller
> >
> > Northwestern University
> >
> > Medical Scientist Training Program
> >
> > cel: 773.608.9185
> >
> > email: j-kell...@northwestern.edu
> >
> > *******************************************
> >
> >
> >
> >
>
>
>
>
