I vote for the electron density irrespective of side chains, main chains,
ligands, dark matter. The PDB is a collection of experimentally determined
structures per its own definition. If density supports it high B is fine -
B-factor simply is a parameter of a probability distribution. If you extend
that to no density - it becomes problematic. After all, coordinates imply
that an atom is actually at some specified place with a certain probability.
We may know that the atom necessarily has to be someplace lest it got chewed
off for some reason. The experiment just tells you that you do not know
where the atom is.
Or in Rumsfeldic: Better a known unknown than a unknown known.
Cheers, BR
-----Original Message-----
From: Boaz Shaanan [mailto:[log in to unmask]]
Sent: Sunday, April 03, 2011 11:02 AM
To: [log in to unmask]; [log in to unmask]
Subject: RE: [ccp4bb] what to do with disordered side chains
The original posting that started this thread referred to side-chains, as
the subject still suggests. Do you propose to omit only side-chain atoms, in
which case you end up with different residues, as pointed out by quite a few
people,or do you suggest also to omit the main-chain atoms of the
problematic residues ?
Besides, as mentioned by Phoebe and others, many users
(non-crystallographers) of PDB's know already the meaning of the B-factor
and will know how to interpret a very high B. It is our task (the
crystallographers) to enllighten those who don't know what the B column in a
PDB entry stands for. I certainly do and I'm sure many of us do so too. I
voted for high B and would vote for it again, if asked.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Bernhard Rupp
(Hofkristallrat a.D.) [[log in to unmask]]
Sent: Sunday, April 03, 2011 7:42 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] what to do with disordered side chains
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
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Northwestern University
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