perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along these lines?
And oblige us all to follow them?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
On 30 Mar 2011, at 17:29, Phoebe Rice wrote:
> I've now polled 4 fairly savvy "end users" of crystal structures and there seems to be a consensus:
>
> - they all know what B is and how to look for regions of high B (with, say, pymol) and they know not to make firm conclusions about H-bonds to flaming red side chains.
> - None of them would ever think to look at occupancy and they don't know how anyway.
> - they expect that loops with disordered backbones would not be included in the models, and can figure out truncated or fake-ala side chains with some additioanl effort, but that option makes viewing surfaces and e-stats more of a pain.
>
> Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
>> Date: Tue, 29 Mar 2011 17:43:49 -0400
>> From: CCP4 bulletin board <[log in to unmask]> (on behalf of Ed Pozharski <[log in to unmask]>)
>> Subject: [ccp4bb] what to do with disordered side chains
>> To: [log in to unmask]
>>
>> 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.
>>
>> --
>> "I'd jump in myself, if I weren't so good at whistling."
>> Julian, King of Lemurs
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