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Dear CCP4ers,
how to treat poorly ordered side chain atoms is a difficult topic with
no real elegant solution to it ...
In former times, I've removed those "invisible" atom, leading to
incomplete structures and lot of complaints from programs that check for
proper connectivity. Over the years, I've decided to keep all side
chain atoms in a rotamer conformation with Occ=1.0 and let the B-factors
inflate. I don't believe, that the few additional parameters will
noticeable influence the refinement. In any case, users have to check
the deposited structure, irrespective of omitted side chain atoms, zero
occupancies or inflated B-factors. By the time when I was working at
Roche, we deposited in-house the corresponding electron density maps
along with our structures and taught our modelers how to judge
structural parts using these maps. The EDS server by Kleywegt and Jones
provides the right information and is a very valuable source!
Best regards,
Dirk.
David Briggs wrote:
I always leave these atoms in, in a preferred rotamer (with
1.0 occupancy!) and let the B-values refine to >100. These high B-values
clearly indicate the issue at hand, and you can colour the model
accordingly.
...assuming the end-user knows what a B-factor is...
If you can't say with certainty that it's there... why detract from the
accuracy of your model by including stuff that isn't in the data.
you are artificially increasing the R-factor of your model by making your
obs:param ratio less favourable.
Altering numbers in a pdb (how many non-structural users check the Occ &
B-factor columns regularly) is less transparent.
If you remove the atoms, any user will spot the problem, and then
(hopefully) read the pdb remarks where (hopefully) you will have a list of
missing atoms or a helpful remark stating that any atoms missing are
missing
because they were not ordered in the structure.
D
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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