Re: [phenixbb] Using a parameter file in GUI

Hi Nat, I attached the file and emailed, but it bounced back, saying waiting for approval. Can you please allow me to post it. Thanks Suba 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb