refinement of a ligand with alternate conformations in one region but not the other.
Dear All, I am refinining a protein-NAD complex structure at ~1.9A resolution. I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule. Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate? Do I need to enter two ligand molecules or do I have to do more elaborate things? Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one? That's three questions for the wizards. Thanks in advance. Pascal Egea UCSF
Hi Pascal,
Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate?
Do I need to enter two ligand molecules or do I have to do more elaborate things?
All you need to do is copy the atoms in multiple conformations and set the "altloc" column 17. For example: HETATM15878 C1 BHO D1256 27.570 38.520 40.214 1.00 27.53 C HETATM15879 C2 BHO D1256 28.853 38.200 39.517 1.00 26.33 C HETATM15880 C3 BHO D1256 28.892 38.373 38.135 1.00 25.37 C HETATM15881 C4 BHO D1256 27.764 38.820 37.463 1.00 27.30 C HETATM15882 C5 BHO D1256 26.572 39.118 38.117 1.00 25.47 C HETATM15883 C6 BHO D1256 26.457 38.972 39.492 1.00 26.90 C HETATM15884 C ABHO D1256 27.381 38.412 41.698 0.50 25.89 C HETATM15885 O1 ABHO D1256 27.250 37.337 42.252 0.50 27.11 O HETATM15886 N ABHO D1256 27.301 39.545 42.391 0.50 27.93 N HETATM15887 O2 ABHO D1256 26.266 39.863 42.994 0.50 25.79 O HETATM15888 C BBHO D1256 27.585 38.324 41.685 0.50 29.66 C HETATM15889 O1 BBHO D1256 28.651 37.997 42.159 0.50 32.42 O HETATM15890 N BBHO D1256 26.491 38.496 42.420 0.50 32.55 N HETATM15891 O2 BBHO D1256 25.358 38.331 41.899 0.50 39.06 O I think coot has helpful tools for creating multiple conformers.
Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one?
Reasonably recent versions of phenix.refine (e.g. 1.4-3) automatically constrain the sum of multiple-conformer occupancies to one. Ralf
Hi Pascal,
Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one?
the way it is implemented in phenix.refine - no, the sum of occupancies of atoms in alternative conformations is constrained to be 1. However, if your constrained group has only one selection, for example: refinement.refine.occupancies { constrained_group { selection = chain A and resseq 123 } } than refined occupancies for all atoms in entry number 123 in chain A will be refined to a number between 0 and 1 and will be equal to each other. Sometime it is useful for refinement of partially occupied ligands. Pavel.
participants (3)
-
Pascal Egea -
Pavel Afonine -
Ralf W. Grosse-Kunstleve