Re: [ccp4bb]: refinement of atoms at special position using refmac5

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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> Jianping Ding wrote:
> 
> Hi there,
> 
> I am trying to use refmac5 to refine a structure at 2.0 A resolution.
> Right now, I have two questions in my refinement that I would need
> your help: 1) How do I refine atoms at special position (I mean at
> crystallographic axes)?  2) How do I refine residues with dual
> conformations?
> 
> Any suggestions and advices are greatly appreciated.
> 
> Thanks in advance!
> 
> 
> Jianping Ding
> 
> 
> 


 In special positions; eg on a 3-fold axis..
Set occ=0.33 ( actually I think REFMAC5 might correct it for you..)

 dual conformations:
Just use the PDB convention for naming..
ATOM    195  CB  GLN B   4     -12.666   2.760   8.116  1.00 39.18
ATOM    194  CG AGLN B   4     -13.007   1.731   7.035  0.60 11.45
ATOM     28  CG BGLN B   4     -12.978   1.763   6.996  0.40 37.30
ATOM    193  CD AGLN B   4     -12.270   0.520   6.830  0.60 12.42
ATOM     27  CD BGLN B   4     -14.070   2.781   6.746  0.40 32.97
ATOM    192  OE1AGLN B   4     -12.812  -0.612   6.494  0.60 17.67
ATOM     26  OE1BGLN B   4     -14.059   3.957   7.112  0.40 40.00
ATOM    191  NE2AGLN B   4     -10.898   0.624   6.949  0.60 28.94
ATOM     25  NE2BGLN B   4     -15.108   2.179   6.165  0.40 35.67