[phenixbb] NAG-NAG link definition seems to have no effect

Nathaniel Echols nechols at lbl.gov
Wed Jun 11 17:12:39 PDT 2014


On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c at 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
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