[ccp4bb]: nucleic acids and alternate conformations within a strand: refmac5

[<wgscott@chemistry.ucsc.edu>]

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I apologize if this has been answered before but my search did not turn 
up anything.

I am refining a nucleic acid, one strand of which has two consecutive 
nucleotides (backbone + ribose + base) that have two alternate 
conformers.

I haven't been able to get refmac5 to allow me to do this.

If I focus on the first of the two, and break the chain so that it 
becomes the 3' end of a chain, rather than an internal nucleotide, I can 
get refmac to refine the two conformations.  However if I make two 
alternative 3' ends that are instead of one residue long, two residues 
long, refmac no longer allows me to do this.  Therefore I think I can 
safely conclude it is a problem with wanting to have more than one 
residue as an alternate conformer, rather than some other sort of syntax 
error.

The error refmac reports in the cases where it doesn't work is:

  ERROR: in chain SS residue: 120
         different residues have the same number


There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error


Any suggestions for a workaround?

Thanks in advance.

Bill Scott