[phenixbb] dummy atom v.s. model with zero occupancy.

[Jinzhong Lin]

On 04/21/2013 01:22 AM, Nathaniel Echols wrote:
> On Sat, Apr 20, 2013 at 7:40 PM, Jinzhong Lin <jzlsci at gmail.com> wrote:
>> I suspect that model will still be used to
>> calculate the Fc even though the occupancy is zero, so the map will be
>> severely model biased.
> Technically, they will be included in the Fc calculation in our
> implementation, but since the occupancy is zero, their contribution to
> Fc will be as well.  So no, model bias should not be a problem.
>
> -Nat
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It is an impression I got from two of my colleagues both of who had 
spent some time  playing with bulk solvent model.

One was trying to add a tRNA into his structure. He could see some 
densities for the tRNA, so he put a tRNA model there, set the occupancy 
to zero and adjusted the setting.
Since the resolution is only 7 A, he only tried rigid body refinement. 
Surprisingly, the resulting map showed an unreasonably good density for 
the tRNA. He put
the tRNA model in a completely different position, he also got the 
density back in that wrong position.

The other person was doing the same thing except this time his model he 
wanted to put in is a small molecule.  The resolution is 4A. He found 
him in the same situation.

I am not sure if they have done things correctly. I am going to do this 
on my own, I will keep you all updated.