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Technically there is nothing against setting the occupancy to zero.
Personally though I think this is bad practice. Many users of the PDB just
look at the structure. They would not read through the remarks of the
PDB-file or check the occupancies for a few thousand atoms.
Coot visibly marks atoms with zero occupancy, but it is the only program I
am aware of which does that.
And since most non-crystallographers probably do not use coot to look at a
structure but are the ones the interprete it, I would remove atoms for
which there is no experimental evidence.
Tim
- --
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 10 Jan 2007, Eleanor Dodson wrote:
I really have no view providing that if you include the whole side chain you
must set the atom occupancy to 0.00 forthe invisible atoms..
Eleanor
Nicholas Noinaj wrote:
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Hi,
i would like to get opinions on whether or not one removes side-chain atoms
where there is no density. for example, if one can only observe density up
to the beta-carbon for lysine (say at > 0.5 sigma), does one leave the
lysine side chain intact, knowing it must be disordered, or does one
terminate at the beta-carbon, making the coordinates reflect what is
actually observed in the density.
It seems both approaches are published and people seem to have conflicting
opinions on the topic. It would be nice to come to some concensus,
possibly clear up the issue for us newbies.
Thanks in advance for all feedback!
Cheers,
NIck
________________________________________
Nicholas Noinaj
University of Kentucky College of Medicine
Department of Molecular and Cellular Biochemistry
The Center for Structural Biology
Biomedical Biological Sciences Research Building, Rm 236
741 S. Limestone
Lexington, Ky 40536
Lab: 859-323-8183
Cell: 859-893-4789
Home: 859-228-0978
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noinaj.com
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