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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