Hi Yuri, yes, Ed is perfectly right - you don't want to refine occupancies of water at this resolution (1.5A). Regarding the ligand: just make sure the occupancies of ligand atoms are all equal to each other and less than 1 (say 0.9) in your input PDB file. The rest will be taken care of automatically. Pavel. On 8/13/11 8:30 AM, Yuri wrote:
Hey, So I am finishing up a model at 1.5 A and I tried to refine my ligands (3) and waters (468) in addition to altloc residues. The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in A have OccA and all the atoms in B have OccB. My ligands on the other are being refined as the following:
HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93 23.77 C C
HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85 24.79 C O
HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70 22.70 C O
HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00 25.46 C C
HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92 28.45 C C
HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00 30.15 C O
HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00 30.23 C O
HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00 30.56 C H
HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56 C H
Each atom is getting an individual occupancy assigned, which physically is impossible :) Any light? Could it be my selection syntax?
Corrigendum: I think I sent a bug email last night about an error when writing mtz files in refinement. It was an accident. My naming convention was bad, thats why it crashed. Sorry