From: Ivan Shabalin
Date: 1 November 2011 22:47
Dear Refmac users,
Im a bit confused how Refmac treats ions. In the monomers library I can find Cl.cif:
CL . 'chlorine ' non-polymer 1 1 .
#
data_comp_CL
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
CL CL CL CL 0.000
It does not have charge and atom.atom_id is CL, but not Cl-1 (I believe, it is important for the scattering factor). I tried to change these fields but refmac crushed.
Searching through CCP4BB I found that Ions from nonions are distinguished by just addition charge on the element column in the PDB file. So, for Cl I have to type Cl-1 in the last field of PDB-file line. I tried and it worked, at least REFMAC uses different coefficients for atomic scattering factor for the ion and B-factors are changed a bit. But I never seen in PDB files that somebody specifies Cl-1 or Mg+2. And when you bring new ligand with Coot id does not specify the charge.
I have two questions:
1) Cl and Cl- have very different atomic radii and the scattering factor coefficients are quite different. But, does it really make significant difference for refining?
2) Is it possible to specify atom type in the library, so that the scattering factor coefficients will be taken into account by Refmac? Or changing PDB-file manually is the only way?
Thank you very much for any comments!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate, University of Virginia
4-224 Jordan Hall, 1340 Jefferson Park Ave.
Charlottesville, VA 22908
----------
From: Garib N Murshudov
Date: 1 November 2011 22:47
Dear Refmac users,
Im a bit confused how Refmac treats ions. In the monomers library I can find Cl.cif:
CL . 'chlorine ' non-polymer 1 1 .
#
data_comp_CL
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
CL CL CL CL 0.000
It does not have charge and atom.atom_id is CL, but not Cl-1 (I believe, it is important for the scattering factor). I tried to change these fields but refmac crushed.
Searching through CCP4BB I found that Ions from nonions are distinguished by just addition charge on the element column in the PDB file. So, for Cl I have to type Cl-1 in the last field of PDB-file line. I tried and it worked, at least REFMAC uses different coefficients for atomic scattering factor for the ion and B-factors are changed a bit. But I never seen in PDB files that somebody specifies Cl-1 or Mg+2. And when you bring new ligand with Coot id does not specify the charge.
I have two questions:
1) Cl and Cl- have very different atomic radii and the scattering factor coefficients are quite different. But, does it really make significant difference for refining?
2) Is it possible to specify atom type in the library, so that the scattering factor coefficients will be taken into account by Refmac? Or changing PDB-file manually is the only way?
Thank you very much for any comments!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate, University of Virginia
4-224 Jordan Hall, 1340 Jefferson Park Ave.
Charlottesville, VA 22908
----------
From: Garib N Murshudov
You do not have to change dictionary. You can specify charges on atoms using element columns in the pdb file. For example:
ATOM 139 O HOH A 35 13.139 -4.487 5.983 1.00 31.43 AA1 O
ATOM 140 CL CL A 35 13.139 -7.487 5.983 1.00 31.43 AA1 CL-1
Regards
Garib
Garib N Murshudov
Structural Studies Division
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
No comments:
Post a Comment