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 [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Sunday, April 03, 2011 7:42 PM
To: CCP4BB@JISCMAIL.AC.UK
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
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu<mailto:j-kell...@northwestern.edu>
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