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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