Thanks

On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty@lbl.gov> wrote:

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 <phenixzyfish@gmail.com> wrote:

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 <nwmoriarty@lbl.gov> wrote:

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 <phenixzyfish@gmail.com> wrote:

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 

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb

--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb

--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov