[buster-discuss] Advice on ncs and target restraints

esserlo at helix.nih.gov esserlo at helix.nih.gov
Sun Dec 14 03:13:51 CET 2014


  this is a question of a buster/tnt novice ...

  I am having a little bit of trouble understanding which residues are
restrained by NCS and independently of NCS, which residues are restrained by
a target that is provided.

I am running 'refine' so far in 'auto' mode.

refine -m data -p model  -target ./Reference/combi.pdb -autoncs

I can see in the LIST.html file in each Cycle-## directory with a link to
auto_gelly_cards.txt the following:

NOTE BUSTER_TARGET01 Reference/combi.pdb
NOTE BUSTER_SET target01set = All
NOTE BUSTER_SIM_DEFINE target01 target01set TARGET01_*

Is this all information about the target restraints ? Is there a way to get
a list that explicitly states which model residue is being restrained by which
target residue (as in phenix.refine) ?

The reason why I ask is that it appears that some restraints for some domains
are not properly applied.
My target "combi.pdb" contains a number of breaks where I know that the
reference is not useful. Could this be a problem ?

Now on to NCS

NOTE BUSTER_SET ncsautoXcld = Water
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|45 A|48 A|53 A|67 A|70 A|73 }

    ...mean that water and the individually listed residue are excluded from
any NCS consideration? - Or are those ranges of residues that are excluded

As much as autoncs is convenient for new users, do experts prefer to define
their own ncs sets still ?



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