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[ccp4bb]: refmac5 geometry restraints



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Dear colleagues:
this is about some trouble I am having with methionine bond lengths. 
This problem is NOT shown on PROCEHECK's geometrical distortion summary 
page but comes up in PDB/ADIT's "validation" summary letter.

Deviation  Residue  Chain  Sequence  AT1  -  AT2    Bond    Dictionary
              Name     ID     Number                 Distance    Value
------------------------------------------------------------------------
   -0.358     MET        A    101      SD   -  CE     1.433     1.791
   -0.228     MET        B    101      SD   -  CE     1.563     1.791
   -0.218     MET        B    132      SD   -  CE     1.573     1.791

When manually corrected (geometry refinement in Xtalview) refmac 
restores the shorter bond distances. My diagonal weighting term is at 
0.25 for 1.8 A data and appears to be a reasonable choice: no other 
significant distortions are found and geometry RMSD are ok.
I looked at $CBIN/data/monomers/mon_lib_prot.cif:

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
  MET        N    H       coval       0.860    0.020
  MET        N    CA      coval       1.458    0.019
  MET        CA   HA      coval       0.980    0.020
  MET        CA   CB      coval       1.530    0.020
  MET        CB   HB1     coval       0.970    0.020
  MET        CB   HB2     coval       0.970    0.020
  MET        CB   CG      coval       1.520    0.030
  MET        CG   HG1     coval       0.970    0.020
  MET        CG   HG2     coval       0.970    0.020
  MET        CG   SD      coval       1.803    0.034
  MET        SD   CE      coval       1.791    0.059
  MET        CE   HE1     coval       0.960    0.020
  MET        CE   HE2     coval       0.960    0.020
  MET        CE   HE3     coval       0.960    0.020
  MET        CA   C       coval       1.525    0.021
  MET        C    O       coval       1.231    0.020

and changed both CG-SD and SD-CE esd's to 0.02 with no effect.
I am using refmac5 as distributed with CCP4-4.2.1 (intel linux).
How can I selectively enforce stronger restraints for selected bonds in 
selected residues?
I am grateful for any suggestions.
Wolfram Tempel
U. of Georgia