Setting the atoms to 0.01 occ seems to have solved the problem.
Thanks to everyone for their help.
best,
Iain
Eleanor Dodson wrote:
> If the occupancy is 0.00 there will be no refinement - the output cds
> are the same as the input, and I guess that will make for horrible
> geometry - COOT will "correct" the geometry of all atoms though so you
> can make a prettier picture - but with no more information content re
> the model if the occupancies stay 0.00
> ..
>
> Eleanor
>
> Iain Kerr wrote:
>> Dear all,
>>
>> I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
>> Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds
>> 0.008A/1.1deg angles.
>>
>> In COOT (0.31) many of the residues whose side chains are (fully or
>> partially) set to 0.00 occupancy have really bad geometry...for want
>> of a better description, the side-chains literally look like they
>> have exploded...a few are intact but have distorted planarity. This
>> occurs in 25 residues out of 480 in the ASU.
>>
>> I have tried:
>>
>> 1. refining without TLS - no change
>> 2. no hydrogens - no change
>> 3. refining OVERall B-factors instead of ISOtropic - overall geometry
>> much worse (rmsd 0.088 bonds)
>> 4. DAMP 0.5 0.5 - no change
>> 5. BABINET scaling instead of SIMPLE - no change in geometry, Rfree
>> and Rfac increase ~3%
>> 6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles)
>>
>> This occurs with two other structures at higher resolution (~2.5A),
>> although only a few violations..it seems to be much worse at low
>> resolution.
>>
>> Any ideas ?
>>
>> Thanks,
>> Iain
>>
>>
>
>
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