[phenixbb] B-factor and phenix.refine+Occ+charge
pafonine at lbl.gov
Thu Jun 23 11:11:55 PDT 2011
some typical things to try in this situation:
- refine occupancy and B of Sn starting with different (reasonable) values;
- make sure the input PDB file contains charge and phenix.refine did
recognize it (check log file as Ralf suggested);
- try refining anisotropic ADP for Sn only.
- a somewhat higher ADP for Sn compared to surrounding atoms is not too
unexpected as it is an "isolated" atom (not covalently bonded to other
atoms), and therefore can be more mobile.
On 6/23/11 9:36 AM, Haytham Wahba wrote:
> June 23, 2011, 9:30 AM
> Dear all
> dimer in AU
> average B factor 21
> resolution: 1.78
> each subunit shows 2 Tin atoms in the active site
> B factor for 2 tin in chain A 15 and 19
> B factor for other 2 tin in chain B 30 and 41
> 41 for tin which is between the 2 cysteine (photo attached) (occ:
> 0.25) this one which i am worry about ((because the average B
> factor for the surrounding amino acid is 20))
> and 30 of the other one near phoshate (occ: 0.70)
> 1- i tried to change the occupancy or refine the occupancy for tin
> trying to reduce B factor (41)
> it works (reduced to 30) but it gives me a +ve peak
> what could i do to solve this problem??
> 2- other trial to define charge for that tin
> HETATM 3241 SN SN C 3 6.543 -2.139 -14.821 0.25 41.55
> but it was the same result.
> --- is this definetion for that charge is OK or it is not enough
> in PDB file
> --- is this way is understandable by phenix.refine?
> i mean does phenix differentiate in refinment between SN, SN2+ and
> N.B: protein soaked in DimethylTindiBromide
> Haytham Wahba
> phenixbb mailing list
> phenixbb at phenix-online.org
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