Alexandra
The restraints refining to a too short a distance is a real problem. The
first thing to do is check in the .geo file to ensure that the restraints
are being set correctly. It is a simple text file so it should be easy to
read.
Feel free to send it to me driectly (with the .pdb file) if you want me to
take a look.
Cheers
Nigel
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Jul 2, 2015 at 9:14 AM, Alexandra Marques
Hi,
I am refining a protein with a Mo in the active site and which is bound to a cofactor and to a water molecule. After each refinement step there is always a lot of positive and negative density around the Mo and the cofactor molecules, although their occupancy refined to 1. I read this message http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html, but I still have doubts about how to choose the refinement parameters. I know I have to select the Mo atoms to be refined anisotropically. And the other atoms, do I have to specifically select them to be refined isotropically?. For instance:
Isotropic atoms: not element Mo
Anisotropic atoms: element Mo
I am asking that because I have been using TLS for the protein atoms during refinement, so I am not sure if it is correct to select the other atoms as isotropic or if I leave it in blank…
My other problem is with the metal restraints. I am not sure about the ideal distance between the Mo and O atom but based on homologous protein structures I choose the following:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name MO and chain A and resname 4MO and resseq 1
atom_selection_2 = name O and chain A and resname O and resseq 2
distance_ideal = 1.900000
sigma = 0.050
}
}
However after the refinement this ideal distance interval (1.95-1.85) is not respected; I have 4 active sites and in some of them the Mo-O distance refines to 0.83 A although there is a lot of density for the water molecule to be at 1.9 A. How to make the restrainst work? Am I missing something?
Thank you very much,
Alexandra
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