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

Pavel Afonine pafonine at lbl.gov
Sun Apr 21 08:52:57 PDT 2013

Hi Lithlin,

I guess I have an idea about what's happening. When you add dummy atoms 
(unstructured or as some model) with zero occupancy and ask the mask to 
not set up bulk-solvent in that region, the (difference) maps you get 
are contrasted in the region of dummy atoms; that is density becomes 
systematically different in that region. Whether that is because of 
genuine feature or classical model bias isn't clear. Perhaps that's not 
limited to difference maps..


On 4/21/13 7:50 AM, Jinzhong Lin wrote:
> 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.
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