Re: [phenixbb] Using a parameter file in GUI

Unless I'm misinterpreting this, it doesn't look like the chelator is bound at all, and the metal ion is either partial occupancy or also missing. The Asp sidechain, on the other hand, does look like it should be coordinating the metal (if present). Try taking the chelator out, fix the sidechain, and re-refine (using metal coordination restraints which ReadySet can provide), and see if the chelator density comes back. If it does, then the Asp sidechain and the chelator will need to be modeled as alternate conformers, where one is "A" and the other "B", so the atoms won't overlap in the nonbonded restraints. On Tue, Feb 7, 2012 at 9:46 AM, Subhani Bandara wrote:

Hi Nat,

I have attached a picture of that area with this. The rotamer I am refering to is ASP 26.

Thanks Subhani

On Mon, Feb 6, 2012 at 5:47 PM, Nathaniel Echols wrote:

...

On Mon, Feb 6, 2012 at 3:42 PM, Subhani Bandara wrote:

...

I have a protein cocrystallized with a metal chelator complex. The side chain of a Asp residue has density around one of the chelators(oxygen atom). The positive density for the rotamer of Asp is seen too close to chelator oxygen(~1.17 A) and therefore rotamer is moving into a negative density.

 When I correct the rotamer and refine, it again come back to the same place, due to repulsive forces I guess. then I moved ligand away and refined with corrected rotamer, but after refinement ligand is again back at the same position, as well as the rotamer. How can I fix this? Does this indicate that the ligand may  not be there although I see some density for it(full density is seen ~0.79 sigma and partial density ~1.00 sigma). Also is this happening due to the memory of ligand position in phenix.

I'm finding this a little difficult to visualize - do you think you could make a picture of it in Coot or PyMOL and post that to the list?  (The server may complain about the message size if it's over 40KB, but the list administrator [me] can approve it for posting anyway.)

thanks, Nat

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