Re: [phenixbb] metal coordination restrain on alternative conformation

Hi Nigel, Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. Thanks Yu On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu wrote:

Thanks

On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty wrote:

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I ran

phenix.metal_coordination

and got the attached. Pass it to phenix.refine.

On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu wrote:

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Hi Nigel,

Thanks. Please see attached PDB file. The structure has two molecules in one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, M, N, O, P, Q, R, and S for molecule 2)

There is only one nucleoside-triphosphate and its cognate MG++ in each molecule having alternative conformations (named as conformation A and B). The desired restrains are as follows,

In molecule 1, atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739 distance_ideal = 2.090000

atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 atom_selection_2 = name O3G, B and chain S and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 atom_selection_2 = name O1B,B and chain S and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 atom_selection_2 = name O1B,A and chain S and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 atom_selection_2 = name O1G,A and chain S and resname CMP and resseq 2001 distance_ideal = 2.090000

In molecule 2, atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739 distance_ideal = 2.090000

atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 atom_selection_2 = name O3G, B and chain I and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 atom_selection_2 = name O1B,B and chain I and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 atom_selection_2 = name O1B,A and chain I and resname CMP and resseq 2001 distance_ideal = 2.090000

atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 atom_selection_2 = name O1G,A and chain I and resname CMP and resseq 2001 distance_ideal = 2.090000

On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty wrote:

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Can you send the residues involved?

Nigel

NB. Any files sent to me will be held in strictest confidence.

On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu wrote:

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Hi everyone,

My structure contains a metal coordinating to some residues, one of which has alternative conformations. Phenix doesn't pickup the residue with alternative conformation when I tried to generate metal restrains using ready.set.

Any idea? Thanks

Yu

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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

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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