Split Occupancy of a ligand and water
Hello, Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick. Thanks for any help!! Brandon -- Brandon Goblirsch Research Assistant-Wilmot Lab Biochemistry, Molecular Biology and Biophysics 5-230 Nils Hasselmo Hall Minneapolis, MN 55455 (612)624-0141
Use different altloc tags in the PDB (Column 18). For example:
HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O
HETATM 2143 O BLIG 1010 7.403 -7.755 -0.773 1.00 29.28 O
Then it will know they don't occupy the same space at the same time. As a
word of warning the occupancy refinement of two proximal atom that don't
have the same residue number can sometimes add up to more than 1 so check to
make sure the model makes physical sense.
Hope this helps,
Katherine
On Mon, Mar 28, 2011 at 2:40 PM, Brandon Goblirsch
Hello,
Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick.
Thanks for any help!!
Brandon -- Brandon Goblirsch Research Assistant-Wilmot Lab Biochemistry, Molecular Biology and Biophysics 5-230 Nils Hasselmo Hall Minneapolis, MN 55455 (612)624-0141 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi,
Use different altloc tags in the PDB (Column 18). For example:
HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O HETATM 2143 O BLIG 1010 7.403 -7.755 -0.773 1.00 29.28 O
Then it will know they don't occupy the same space at the same time. As a word of warning the occupancy refinement of two proximal atom that don't have the same residue number can sometimes add up to more than 1 so check to make sure the model makes physical sense.
if you assign them the same residue number, in the example above that would be HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O HETATM 2143 O BLIG 1009 7.403 -7.755 -0.773 1.00 29.28 O then the sum of occupancies occupancy(AHOH) + occupancy(BLIG) will be 1 exactly. Please let me know if it is not the case. An example of similar thing is: http://www.rcsb.org/pdb/files/1EJG.pdb see residue number 22 for example. Although that software didn't do it quite right (I mean occupancy grouping and constraining). Pavel.
Hi Brandon, you can do it - see two previous replies. If you still have any questions or problems then you can send me a PDB file, explain what and how you want to refine (point out relevant atoms, and how their occupancies are expected to be coupled), and then I will send you back a working example. Pavel. On 3/28/11 12:40 PM, Brandon Goblirsch wrote:
Hello,
Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick.
Thanks for any help!!
Brandon
participants (3)
-
Brandon Goblirsch -
Katherine Sippel -
Pavel Afonine