On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c@gmail.com> wrote:

I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI),

apply_cif_link {
data_link = "NAG-ASN"
residue_selection_1 = "chain A and resname NAG and resid 401"
residue_selection_2 = "chain A and resname ASN and resid 74"

}
apply_cif_link {
data_link = "BETA1-4"
residue_selection_1 = "chain A and resname NAG and resid 401"
residue_selection_2 = "chain A and resname NAG and resid 402"

}

Okay, I think this may be part of the problem - you are missing the outer "scope" for these parameter blocks, so they are not processed correctly. If you change "apply_cif_link" to "refinement.pdb_interpretation.apply_cif_link" in both places it may fix the problem.

Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant)

Sorry, this is actually my bug (those atoms should not be included in covalently linked sugars), and I think I still have an email complaining about this in my inbox from late 2012. I need to overhaul that bit of code anyway so I will see if Nigel and I can come up with something smarter.

-Nat