Hi, I am trying to solve a structure of a protein that is cocrystallized with a chelator complex using phenix (GUI). The complex is Tb(DPA)3 and DPA stands for dipicolinic acid. In the structure (C222) there are few Tb complexes on the two fold axis with symmetry coordinates 1/4X, 1/4Y, Z. In those, Tb and the center C (C4) and N (N1) of one DPA are sitting directly on the 2 fold axis. So I left only half of that DPA ligand structure on PDB file and changed the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00. Then I refined it while keeping above occupancies and xyz coordinated of the ligand fixed. After doing this the other half of the ligand could be built by symmetry, but it left a space between two halves(so it was not as one ligand). Can you please let me know what I can do to fix this structure. Also is there a way to keep only x and y coordinates fixed while varying z during refinement. Thanks Subhani
So I left only half of that DPA ligand structure on PDB file and changed the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00.
Keep the occupancy of N1 and C4 as 1.00, then phenix.refine should automatically detect those as special positions and keep them exactly on the two-fold axis. The bonds and other restraints to the atoms on special positions will not work automatically. Currently, the only option is to define custom bonds (see phenix.refine docs) with symmetry_operation=x,y,z. You can use Coot to obtain the symmetry operation (turn on drawing of symmetry copies; when clicking atom Coot will show the sym op). Emulate angle and dihedral restraints with pseudo-bonds. Inspect the .geo file to verify that all restraints are correct. You can also keep all DPA atoms, with all occupancies set to 0.5. Then the restraints will work as usual; probably you don't have to do anything special. However, the N1 and C4 are allowed to float around the special position. It may be OK though. I think I'd try this option first. Ralf
Hi Ralf, Thanks a lot for the fast response. I have actually tried setting all occupancies to 0.5 and it didn't work. Also I could find how to define custom bonds, but I am not clear with how to use symmetry operations and pseudo bonds (I know how to turn on symmetry in coot). Following are the commands I came up with for custom bonds refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain y and resseq 2 and name N1 atom_selection_2 = chain y and resseq 2 and name C4 distance_ideal = 3.0 sigma = 0.02 slack = None } bond { action = *add atom_selection_1 = chain y and resseq 2 and name N1 atom_selection_2 = chain Z and resseq 1 and name TB distance_ideal = 2.5 sigma = 0.02 slack = None } } Also if I want to run refine in GUI can I give these commands as an input file? If so what is the file format I should use? Thanks in advance Subhani On Mon, Oct 17, 2011 at 2:50 PM, Ralf Grosse-Kunstleve < [email protected]> wrote:
So I left only half of that DPA ligand structure on PDB file and changed
the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00.
Keep the occupancy of N1 and C4 as 1.00, then phenix.refine should automatically detect those as special positions and keep them exactly on the two-fold axis. The bonds and other restraints to the atoms on special positions will not work automatically. Currently, the only option is to define custom bonds (see phenix.refine docs) with symmetry_operation=x,y,z. You can use Coot to obtain the symmetry operation (turn on drawing of symmetry copies; when clicking atom Coot will show the sym op). Emulate angle and dihedral restraints with pseudo-bonds. Inspect the .geo file to verify that all restraints are correct.
You can also keep all DPA atoms, with all occupancies set to 0.5. Then the restraints will work as usual; probably you don't have to do anything special. However, the N1 and C4 are allowed to float around the special position. It may be OK though. I think I'd try this option first.
Ralf
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On Wed, Oct 19, 2011 at 11:19 AM, Subhani Bandara
Also if I want to run refine in GUI can I give these commands as an input file? If so what is the file format I should use?
Yes, just save them to a plain-text file and add it to the list of input files in the first tab. It will probably work best if you use one of the filename extensions .eff, .def, or .phil. -Nat
participants (3)
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Nathaniel Echols -
Ralf Grosse-Kunstleve -
Subhani Bandara