Hi Andreas I can't explain your first problem, but I may be able to explain your second one.
My take from the Refmac code is that a VDW repulsion restraint between any pair of atoms is included ONLY if the atoms are NOT bonded or related by a bond angle (obviously) OR the occupancy sum is > 1.0001 OR (the alt codes are equal AND the internal residue numbers are equal AND they belong to the same symmetry instance). So in your first example, unless the residue numbers of ALIG & BLIG are different or they are from different symmetry instances (both unlikely I guess) then they shouldn't be repelled. So it would seem that there must be a reason other than VDW restraints that they are moving apart, though I can't say what that reason might be. In your second example the occupancy sum of BTRP and BLIG is exactly 1 (i.e. <= 1.0001) and though the alt codes are the same, they presumably have different internal residue numbers so there is no repulsion restraint according to the test above, despite the fact that there "obviously" should be one. In other words alt codes are designed to handle disorder within a residue, NOT between different residues/ligands, though in principle it could be done, e.g. by removing the test on residue numbers. One would then need to take care that the disorder of groups with the same alt code was in fact correlated, also there might be complications if say the occupancy of ATRP/BTRP refined to 0.5/0.5 but that of ALIG/BLIG refined to 0.7/0.3. Then obviously you couldn't say that there's necessarily a correlation between the alternate positions of TRP & LIG. Cheers -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Andreas Hörnberg > Sent: 14 June 2007 09:24 > To: [email protected] > Subject: Problem with ligand refinement in REFMAC5 > > Dear all! > > I have two questions: > > First - I am refining a structure containing a modified residue with a > ligand bound. This ligand is present in two stereoisomers and it seems > like we have both in the structure. When refining the > structure with ALIG > and BLIG (each with 0.5 occupancy) defined in the coordinate > file, REFMAC5 > moves the ligands apart. In the ligand there is an electron > rich atom with > a clearly defined position in the electron density map (observed at 9 > sigma). Prior to refinement, the electron rich atom from the two > stereoisomers are positioned in the centre of the strong > density feature. > After ten cycles of refinement the atoms are separated (by > about 1 Å) and > found in two different positions, neither of them coinciding with the > strong density. I don't understand why the stereoisomers are > moved apart. > The REFMAC log file does not give any warnings about close contacts > between the atoms, but still they are moved during refinement > and I don't > know how to avoid this! Any help is much appreciated! > > > To contribute to the confusion, the second problem is > actually quite the > opposite... > > I have a non-covalent ligand bound in two alternative, partly > overlapping > sites. The sites induce distinct structural changes of the > protein. For > example, a Trp is moved to sandwich the ligand in one of the > sites whereas > this conformation of the Trp is not consistent with the second binding > site. > > I've tired to refine this structure using REFMAC5 and naming the Trp > ATRP/BTRP and the corresponding ligand ALIG/BLIG in the > coordinate file. > Since the ATRP density map is stronger, the BTRP moves towards this > density, even though this is create clashes between the BTRP > and the BLIG. > The program doesn't seem to link the two sites of the ligand with the > corresponding conformations of the Trp. > > Is it possible to link the ALIG to the ATRP conformation of > the protein > and ligand? > > Sincerely, > > Andreas > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. 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