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Hello Julia--
> I am trying to solve a small helical protein NMR structure using
> XPLOR-NIH. The 3 N- and 5 C-terminal residues are dynamic and I have no
> NOE or dihedral restraints for them, but XPLOR-NIH is extending the
> adjacent helix into these regions in many of the structures that I
> calculate. Is this a common phenomenon and is there a way that I could
> prevent it?
This is most likely caused by the RAMA database potential. To enable
these restraints for a subregion of the protein, replace the
initRamaDatabase() line with:
xSim = xplor.simulation
outputState=xSim.disableOutput()
from selectTools import numResidues
protocol.updatePseudoAtoms(xSim)
global nRama
nRama=45*numResidues( AtomSel('not PSEUDO',xSim) )
print ' allocating space for %d RAMA restraints' % nRama
xSim.command("""
eval ($krama=1.)
rama
nres=%d
end
"""% nRama)
xSim.command("""
rama
@QUARTS:2D_quarts_new.tbl
@QUARTS:3D_quarts_new.tbl
@QUARTS:forces_torsion_prot_quarts_intra.tbl
end
vector identify (store2) (resid 30:70)
@setup_quarts_torsions_intra_2D3D_sel.tbl
""")
xSim.enableOutput(outputState)
where the file setup_quarts_torsions_intra_2D3D_sel.tbl is attached and
should be placed in the directory you're running from. You will need to
modify the atom selection ATOMSEL to the ordered region of your protein,
for example resid 20:100.
Please let me know how this works and I'll add this facility to the
standard setup.
!
! setup_quarts_torsion_intra.tbl
!
! Automatically enters delphic torsion restraints for proteins.
! Based on the maximum-dimensionality classes.
!
!
!
!
!
! select the Cas of the residues you want to create delphic torsion
! assignments for here
!
!fill this in beforehand
!vector identify (store2) (all)
!
! select all cis-prolines here
! fix this
!
vector identify (store6) (resn cisp)
!
! need to select all the residues that immediately preceed a proline
! in order to designate them "xpr"
!
! xpr residues are stored in the store7 array
!
vector do (store7 = 0) (all)
for $count in id (name ca and resn pro) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = decode($result))
eval ($prevRes = $curRes - 1)
vector identify (store7) (store7 or (resid $prevRes and segid $curSeg))
end loop database
!set echo off message off end
!
! these are the groups--cis residues should be eliminated from these selections
!
vector do (store1 = 1) (resn glu or resn ala or resn leu or resn met or resn
gln or
resn lys or resn arg or resn his)
vector do (store1 = 2) (resn val or resn ile or resn tyr or resn cys or resn
trp or
resn phe or resn thr)
vector do (store1 = 3) (resn asn or resn ser or resn asp)
vector do (store1 = 4) (resn gly)
vector do (store1 = 5) (resn pro)
!
!
! ala
!
for $count in id (name ca and resn ala and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class ala_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
end loop database
!
! arg
!
for $count in id (name ca and resn arg and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class arg_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class arg_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class arg_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
end
rama
class arg_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
end
rama
class arg_chi3_chi4
assign
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
(segid $curSeg and resid $curRes and name cz)
end
rama
class arg_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
end
rama
class arg_chi2_chi3_chi4
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ne)
(segid $curSeg and resid $curRes and name cz)
end
end loop database
!
! asn
!
for $count in id (name ca and resn asn and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class asn_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class asn_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class asn_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name od1)
end
end loop database
!
! asp
!
for $count in id (name ca and resn asp and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class asp_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class asp_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class asp_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name od1)
end
end loop database
!
! cys
!
for $count in id (name ca and resn cys and not store7 and store2) loop database
vector show elem (resn) (name sg and bondedto (byresidue id $count and name sg))
if ($select = 0) then
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class cys_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class cys_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
end
end if
end loop database
!
! disulfide
!
for $count in id (name ca and resn cys and not store7 and store2) loop database
vector show elem (resn) (name sg and bondedto (byresidue id $count and name sg))
if ($select = 1) then
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
vector show elem (segid) (name sg and bondedto (name sg and resid $curRes
and segid $curSeg))
eval ($otherSeg = $result)
vector show elem (resid) (name sg and bondedto (name sg and resid $curRes
and segid $curSeg))
eval ($otherRes = $result)
rama
class dis_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class dis_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
end
rama
class dis_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
end
rama
class dis_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $otherSeg and resid $otherRes and name cb)
end
rama
class dis_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $otherSeg and resid $otherRes and name cb)
end
rama
class dis_chi2_chi3_chi4
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $otherSeg and resid $otherRes and name cb)
(segid $curSeg and resid $curRes and name sg)
(segid $otherSeg and resid $otherRes and name sg)
(segid $otherSeg and resid $otherRes and name cb)
(segid $otherSeg and resid $otherRes and name ca)
end
end if
end loop database
!
! gln
!
for $count in id (name ca and resn gln and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class gln_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class gln_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
end
rama
class gln_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name oe1)
end
rama
class gln_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name oe1)
end
end loop database
!
! glu
!
for $count in id (name ca and resn glu and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class glu_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class glu_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
end
rama
class glu_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name oe1)
end
rama
class glu_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name oe1)
end
end loop database
!
! gly
!
for $count in id (name ca and resn gly and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class gly_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
end loop database
!
! his
!
for $count in id (name ca and resn his and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class his_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class his_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class his_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name nd1)
end
end loop database
!
! ile
!
for $count in id (name ca and resn ile and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class ile_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class ile_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg1)
end
rama
class ile_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg1)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg1)
(segid $curSeg and resid $curRes and (name cd or name cd1))
end
end loop database
!
! leu
!
for $count in id (name ca and resn leu and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class leu_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class leu_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class leu_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd1)
end
end loop database
!
! lys
!
for $count in id (name ca and resn lys and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class lys_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class lys_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class lys_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
end
rama
class lys_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
end
rama
class lys_chi3_chi4
assign
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
(segid $curSeg and resid $curRes and name nz)
end
rama
class lys_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
end
rama
class lys_chi2_chi3_chi4
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd)
(segid $curSeg and resid $curRes and name ce)
(segid $curSeg and resid $curRes and name nz)
end
end loop database
!
! met
!
for $count in id (name ca and resn met and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class met_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class met_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class met_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name sd)
end
rama
class met_chi2_chi3
assign
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name sd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name sd)
(segid $curSeg and resid $curRes and name ce)
end
rama
class met_chi1_chi2_chi3
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name sd)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name sd)
(segid $curSeg and resid $curRes and name ce)
end
end loop database
!
! phe
!
for $count in id (name ca and resn phe and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class phe_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class phe_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class phe_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd1)
end
end loop database
!
! pro
!
for $count in id (name ca and resn pro and not store7 and store2 and not
store6) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class pro_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class pro_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class pro_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd1)
end
end loop database
!
! ser
!
for $count in id (name ca and resn ser and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class ser_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class ser_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name og)
end
end loop database
!
! thr
!
for $count in id (name ca and resn thr and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class thr_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class thr_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name og1)
end
end loop database
!
! trp
!
for $count in id (name ca and resn trp and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class trp_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class trp_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class trp_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd1)
end
end loop database
!
! tyr
!
for $count in id (name ca and resn tyr and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class tyr_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class tyr_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
end
rama
class tyr_chi1_chi2
assign
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg)
(segid $curSeg and resid $curRes and name cd1)
end
end loop database
!
! val
!
for $count in id (name ca and resn val and not store7 and store2) loop database
vector show elem (segid) (id $count)
eval ($curSeg = $result)
vector show elem (resid) (id $count)
eval ($curRes = $result)
eval ($nextRes = encode(decode ($curRes) + 1))
eval ($prevRes = encode(decode ($curRes) - 1))
rama
class val_phi_psi
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
end
rama
class val_phi_psi_chi1
assign
(segid $curSeg and resid $prevRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name c)
(segid $curSeg and resid $nextRes and name n)
(segid $curSeg and resid $curRes and name n)
(segid $curSeg and resid $curRes and name ca)
(segid $curSeg and resid $curRes and name cb)
(segid $curSeg and resid $curRes and name cg1)
end
end loop database
!
! finis
!
set echo $prev_echo message $prev_messages end
best regards--
Charles
- --
Charles Schwieters email: [email protected]
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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