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As an update, this approach did not work in Refmac, but as Pavel suggested it worked fine with phenix.refine. --paul On 08/23/2013 11:51 AM, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Paul, > > have you actually tried using the 'alternate location indicator' with > two different residues? I would not be surprised if that would work > with refmac. > > Best, > Tim > > On 08/23/2013 05:39 PM, Paul Paukstelis wrote: >> Greetings, >> >> We have been working on a few DNA crystals in which the asymmetric >> unit contains a stoichiometric (or nearly so) mixture of two >> similar but distinct oligonucleotides. The resolution is medium to >> low (2.7-2.8) but for a few of these there are some hints from the >> density for two different bases at the same position. I'm curious >> what the best way to approach refinement would be in this case. >> Alternate conformation doesn't really work since the residues have >> different nucleobases. Having two complete chains with 0.5 >> occupancy is overkill since there are only 2 (or 4) positions in >> which the sequence differs. I tried just adding a second chain for >> the varying residues at 0.5 occupancy and adding link records to >> the original chain, however this doesn't seem to respect geometry >> of the phosphodiester for the flanking residues. I would appreciate >> suggestions or any examples in the PDB that might set me in the >> right direction. >> >> --paul >> > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.14 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFSF4T7UxlJ7aRr7hoRAtC9AKCeIcRnKeCrsW4/QY7ad5xooRw73wCgvEpw > ite155+O8JylmpSS454gYXM= > =3lH/ > -----END PGP SIGNATURE-----