Judging from some examples in the literature, if there's no density for the ligand, you publish in Nature!
On 31 Mar 2011, at 14:32, Huanwang Yang wrote:
> If a part of sequence has no density, this part will be cut from coordinates.
> If the side chain of a residue is lack of density, the opinion is not converged.
> What about the ligand, if no density is observed?
>
> Huanwang
>
> Ed Pozharski wrote:
>> The results of the online survey on what to do with disordered side
>> chains (from total of 240 responses):
>>
>> Delete the atoms 43%
>> Let refinement take care of it by inflating B-factors 41%
>> Set occupancy to zero 12%
>> Other 4%
>>
>> "Other" suggestions were:
>>
>> - Place atoms in most likely spot based on rotomer and contacts and
>> indicate high positional sigmas on ATMSIG records
>> - To invent refinement that will spread this residues over many rotamers
>> as this is what actually happened
>> - Delet the atoms but retain the original amino acid name
>> - choose the most common rotamer (B-factors don't "inflate", they just
>> rise slightly)
>> - Depends. if the disordered region is unteresting, delete atoms.
>> Otherwise, try to model it in one or more disordered model (and then
>> state it clearly in the pdb file)
>> - In case that no density is in the map, model several conformations of
>> the missing segment and insert it into the PDB file with zero
>> occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS
>> - I would assumne Dale Tronrod suggestion the best. Sigatm labels.
>> - Let the refinement inflate B-factors, then set occupancy to zero in
>> the last round.
>>
>> Thanks to all for participation,
>>
>> Ed.
>>
>>
------
Randy J. Read
Department of Haematology, University of Cambridge
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