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
On Sun, Apr 3, 2011 at 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.)
<[log in to unmask]> 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
>
> =====================================================
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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: [log in to unmask]
>
> *******************************************
>
>
>
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
*******************************************
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