[phenixbb] Split Occupancy of a ligand and water

Pavel Afonine pafonine at lbl.gov
Mon Mar 28 14:42:25 PDT 2011


  Hi,

> Use different altloc tags in the PDB (Column 18). For example:
>
> HETATM 2142  O  AHOH  1009       1.332 -11.668  14.957  0.50  6.57           O
> HETATM 2143  O  BLIG  1010       7.403  -7.755  -0.773  1.00 29.28           O
>
> Then it will know they don't occupy the same space at the same time. 
> As a word of warning the occupancy refinement of two proximal atom 
> that don't have the same residue number can sometimes add up to more 
> than 1 so check to make sure the model makes physical sense.

if you assign them the same residue number, in the example above that 
would be

HETATM 2142  O  AHOH  1009       1.332 -11.668  14.957  0.50  6.57           O
HETATM 2143  O  BLIG  1009       7.403  -7.755  -0.773  1.00 29.28           O


then the sum of occupancies occupancy(AHOH) + occupancy(BLIG) will be 1 
exactly. Please let me know if it is not the case.

An example of similar thing is:
http://www.rcsb.org/pdb/files/1EJG.pdb
see residue number 22 for example. Although that software didn't do it 
quite right (I mean occupancy grouping and constraining).

Pavel.




More information about the phenixbb mailing list