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I do not see how an atom of occupancy 0 would alter the R-factor of your
structure, and I am sure that all refinement programs take that into
proper account - I assume the occupancy is just a weighting factor, so the
atom does not contribute to the R-factor calculation.
And how many non-crystallographers do you know that check the PDB-file,
even by colouring it by B-factor? And how many of them do you think would
interprete the colour scheme correctly?
In my opinion depositing a PDB-file offers a service to a wide community
of researchers and one should make sure that the data it represents are
used as fool-proof as possible (no, I am not calling
non-crystallographers fools). Looking at a residue with missing atoms at
least is something striking.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 10 Jan 2007, Flip Hoedemaeker wrote:
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Hmm, I'd like to stay as close as possible to the biological "truth"... In
this case, you know that the lysine side chain atoms are there but you just
can't see them! 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.
Obviously, for missing loops or ends the situation is a bit different, as
you might have lossed them due to proteolysis, and it is impossible to model
them in without data.
I think putting atoms in with 0 occupancy only confuses users, and you
artificiallly lower the R values of the structure.
Flip
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
Eleanor Dodson
Sent: Wednesday, January 10, 2007 12:21
To: [EMAIL PROTECTED]
Cc: ccp4bb@dl.ac.uk
Subject: Re: [ccp4bb]: Modelling disordered side-chains
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
[EMAIL PROTECTED]
noinaj.com
