Hi,
it is quite possible to truncate say Lys residue isnt it? so why not
do this, this doesn't change
the identity of the residue but precisely draws attention to the fact
that atoms are missing due to lack
of density.
And if you click on an atom in Pymol, at least i dont see the b-factor
displayed anywhere - i would suspect
its the same case with other mol. graphics visualization software to
fair extent. or its some small print somewhere...
+ can you actually tell by just looking at the B-factor whether there
is any density or not? if the wilson b
is high i suspect you can see density and the B-factor will be high
where as if Wilson B is low same b-factor
will probably mean you dont see density at same sigma cutoff/contour
level. or i may be wrong but suspect
this is the case....which is why i think its better probably to
truncate (not to ala/gly, but to truncate) them if
you don't see the density for the side chain at all. OR model the 5
most like conformers then - or 4 - 6 ? 3?
well, this can go on forever --or rather hopefully NOT, but really i
don't think this quite so simple as what comes to
B-factors and later analysis ---in particular if that will be in
anyway automated and will deal with say a larger set of
coordinate files. is it really a good idea to leave an active site
residue side chain with high B (=no density what so ever)
in, in _one_ defined conformation? i am not so dead certain...
cheers,
Tommi
On Apr 3, 2011, at 9:01 PM, Boaz Shaanan wrote:
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>
*******************************************
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
