Dear Sasha,
you should bear in mind that the major part of users of your deposited
structure will not be crystallographers, and they probably don't know
what e.g. a B-value is. So also may no use Coot to visualise the
structure hence may not be pointed at graphically that occupancies are
set to zero.
E.g. I have the impression that sometimes people running molecular
dynamics simulations take a PDB file for granted and as absolute truth,
even irrespective of the resolution and other quality indicators.
Therefore you are on the safe side to delete side chains for which you
don't see density. When you place them, you decide for a position
without experimental evidence.
You can run two tests:
1) remove the side chain and refine. Does the difference map indicate
where the side chain should be? Put it back, otherwise leave it out
The difference density is a little more sensitive than the direct map.
2) place the side chain a little bit, e.g. select a different rotamer in
Coot that does not clash. Then refine. Does the side chain go back to
where you initially placed it? Then there may be some signal in the data
supporting that position. Otherwise, leave it out.
Best,
Tim
On 11/11/2014 02:14 PM, Sasha Pausch wrote:
> Dear CCP4bb,
>
> Sorry for asking a naive question.
>
> I am trying to deposit a structure in PDB. I would like to know whether we
> have to delete the side chains of amino acids for which we are not finding
> density or people prefer keeping the side chains occupancy zero? Is there
> any other way to do this?
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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