ncs resraints: weight-ncs

Gerard 'CD' Kleywegt GERARD at XRAY.BMC.UU.SE
Sat Nov 25 13:16:31 EST 1995


 I thought virus people always constrained their NCS ???  Not sure
 if restraints are a good idea there (unless you have very compelling
 reasons to be believe that there is a significant breakdown of
 the NCS).

 In general, using an NCS weight of 500 will in practice give you
 more or less identical molecules (rmsd ~0.02-0.05 A would be my
 guess).

 Below is an example of how I tend to use NCS restraints, i.e.
 with four classes: main chain ncs and non-ncs, and side chain
 ncs and non-ncs.

 --Gerard

 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 { Filename: ncs_restraints.xplor }

 REMARK Two-fold NCS-restraints for CBH II complexes at 1.8 - 2.2 A resolution

 { use some identity arrays for the selections }

 { STORE1 = all non-hydrogen protein atoms }
 vector ident (store1) ((segid = "AAAA" or segid = "BBBB") and (not hydrogen)
                         and (not resid 85:86))

 { STORE2 = protein backbone }
 vector ident (store2) (store1 and ( name ca or name n or name c or name o
                        or name ot1 or name ot2 ))

 { STORE3 = side chains }
 vector ident (store3) (store1 and (not store2))

 { STORE4 = main chain with possible NCS-breakdown or disorder }
 { derived by inspection of maps, xtal contacts & B factors    }
 vector ident (store4) (store2 and ( resi 86:88 or resi 96:98 or
                     resi 105:111 or resi 114:123 or resi 155:162 or
                     resi 288:290 or resid 309:311 or resi 405:412 or
                     resi 445:447 ))

 { STORE5 = side chains with possible NCS-breakdown or disorder }
 { derived by inspection of maps, xtal contacts & B factors     }
 vector ident (store5) (store3 and ( resi 86 or resi 89
   or resi 116:121 or resi 129 or resi 140:141 or resi 144 or resi 147 or resi 156:161
   or resi 182 or resi 186 or resi 189 or resi 194 or resi 204 or resi 208
   or resi 237 or resi 240 or resi 244 or resi 281 or resi 294 or resi 313
   or resi 319 or resi 344 or resi 356 or resi 362:363 or resi 382 or resi 406:411
   or resi 426 or resi 446:447 or resn="SER" ) )

 ncs restraints

  { (1) normal NCS protein backbone -> tight }
  group equi (segid "AAAA" and store2 and (not store4))
        equi (segid "BBBB" and store2 and (not store4))
        weight-ncs=100.0
        sigb=3.0
  end

  { (2) non-NCS protein backbone -> lax }
  group equi (segid "AAAA" and store2 and store4)
        equi (segid "BBBB" and store2 and store4)
        weight-ncs=5.0
        sigb=5.0
  end

  { (3) normal NCS protein sidechains -> fairly tight }
  group equi (segid "AAAA" and store3 and (not store5))
        equi (segid "BBBB" and store3 and (not store5))
        weight-ncs=50.0
        sigb=3.0
  end

  { (4) non-NCS side chains -> unrestrained }

  ?

 end

 flags include ncs ? end
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----



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