| ! flexref.cns |
| ! The HADDOCK semi-flexible refinement in torsion angle space |
| ! This version supports only distance and symmetry/ncs restraints |
| ! |
| ! *********************************************************************** |
| ! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * |
| ! * All rights reserved. * |
| ! * This code is part of the HADDOCK software and governed by its * |
| ! * license. Please see the LICENSE file that should have been included * |
| ! * as part of this package. * |
| ! *********************************************************************** |
|
|
| if ( $log_level = "verbose" ) then |
| set message=all echo=on end |
| elseif ( $log_level = "normal" ) then |
| set message=normal echo=off end |
| else |
| set message=off echo=off end |
| end if |
|
|
| !==================================================================! |
| ! Initialisation of variables |
| !==================================================================! |
|
|
| evaluate ($saprotocol.randrot=$randrot) |
| evaluate ($saprotocol.separate=$separate) |
| evaluate ($saprotocol.tadhigh_t=$temp_high) |
| evaluate ($saprotocol.t1_init=$temp_cool1_init) |
| evaluate ($saprotocol.t2_init=$temp_cool2_init) |
| evaluate ($saprotocol.t3_init=$temp_cool3_init) |
| evaluate ($saprotocol.t1_final=$temp_cool1_final) |
| evaluate ($saprotocol.t2_final=$temp_cool2_final) |
| evaluate ($saprotocol.t3_final=$temp_cool3_final) |
| evaluate ($saprotocol.inter_init_rigid=$sinter_rigid_init) |
| evaluate ($saprotocol.inter_fin_rigid=$sinter_rigid_final) |
| evaluate ($saprotocol.inter_init_cool2=$sinter_cool2_init) |
| evaluate ($saprotocol.inter_fin_cool2=$sinter_cool2_final) |
| evaluate ($saprotocol.inter_init_cool3=$sinter_cool3_init) |
| evaluate ($saprotocol.inter_fin_cool3=$sinter_cool3_final) |
| evaluate ($saprotocol.tempstep=50) |
| evaluate ($saprotocol.timestep=$timestep) |
| evaluate ($saprotocol.tadfactor=$tadfactor) |
| evaluate ($saprotocol.initiosteps=$mdsteps_rigid) |
| evaluate ($saprotocol.cool1_steps=$mdsteps_cool1) |
| evaluate ($saprotocol.cool2_steps=$mdsteps_cool2) |
| evaluate ($saprotocol.cool3_steps=$mdsteps_cool3) |
| evaluate ($saprotocol.fbeta=100) |
| evaluate ($saprotocol.mass=100) |
|
|
| evaluate ($data.ncomponents=$ncomponents) |
|
|
|
|
| ! non-bonded parameter set to use |
| evaluate ($toppar.par_nonbonded = "OPLSX") |
|
|
| ! dihedrals, DNA and distance restraints |
| evaluate ($Data.dnarest =$dnarest_on) |
| evaluate ($Data.flags.cdih =$dihedrals_on) |
| evaluate ($Data.cdih.on =$dihedrals_on) |
| evaluate ($Data.ssdihed =$ssdihed) |
| evaluate ($Data.error_dih =$error_dih) |
| evaluate ($data.dihedrals.on=$dihedrals_on) |
| evaluate ($data.dihedrals_hot=$dihedrals_hot) |
| evaluate ($data.dihedrals_cool1=$dihedrals_cool1) |
| evaluate ($data.dihedrals_cool2=$dihedrals_cool2) |
| evaluate ($data.dihedrals_cool3=$dihedrals_cool3) |
|
|
| ! planarity restraints |
| evaluate ($Data.flags.plan = false) |
|
|
| ! distance restraints |
| evaluate ($Data.flags.noe = true) |
| evaluate ($data.unambig_hot=$unambig_hot) |
| evaluate ($data.unambig_cool1=$unambig_cool1) |
| evaluate ($data.unambig_cool2=$unambig_cool2) |
| evaluate ($data.unambig_cool3=$unambig_cool3) |
| evaluate ($data.randremoval=$randremoval) |
| evaluate ($data.npart=$npart) |
|
|
| evaluate ($data.ambig_hot=$ambig_hot) |
| evaluate ($data.ambig_cool1=$ambig_cool1) |
| evaluate ($data.ambig_cool2=$ambig_cool2) |
| evaluate ($data.ambig_cool3=$ambig_cool3) |
|
|
| evaluate ($data.hbond_hot=$hbond_hot) |
| evaluate ($data.hbond_cool1=$hbond_cool1) |
| evaluate ($data.hbond_cool2=$hbond_cool2) |
| evaluate ($data.hbond_cool3=$hbond_cool3) |
|
|
| evaluate ($data.mrswi_hot=$mrswi_hot) |
| evaluate ($data.mrswi_cool1=$mrswi_cool1) |
| evaluate ($data.mrswi_cool2=$mrswi_cool2) |
| evaluate ($data.mrswi_cool3=$mrswi_cool3) |
|
|
| evaluate ($data.rswi_hot=$rswi_hot) |
| evaluate ($data.rswi_cool1=$rswi_cool1) |
| evaluate ($data.rswi_cool2=$rswi_cool2) |
| evaluate ($data.rswi_cool3=$rswi_cool3) |
|
|
| evaluate ($data.masy_hot=$masy_hot) |
| evaluate ($data.masy_cool1=$masy_cool1) |
| evaluate ($data.masy_cool2=$masy_cool2) |
| evaluate ($data.masy_cool3=$masy_cool3) |
|
|
| evaluate ($data.asy_hot=$asy_hot) |
| evaluate ($data.asy_cool1=$asy_cool1) |
| evaluate ($data.asy_cool2=$asy_cool2) |
| evaluate ($data.asy_cool3=$asy_cool3) |
|
|
| evaluate ($data.cmrest=$cmrest) |
| evaluate ($data.cmtight=$cmtight) |
| evaluate ($data.kcm=$kcm) |
| evaluate ($data.kcont=$kcont) |
| evaluate ($data.contactairs=$contactairs) |
| if ($data.contactairs eq true) then |
| evaluate ($data.randremoval = false) |
| end if |
|
|
| ! NCS restraints |
| evaluate ($data.kncs = $kncs) |
| evaluate ($Data.flags.ncs = $ncs_on) |
| evaluate ($data.nncs = $nncs) |
|
|
| ! Symmetry restraints |
| evaluate ($data.ksym = $ksym) |
| evaluate ($Data.flags.sym = $sym_on) |
| evaluate ($data.nc2sym = $nc2sym) |
| evaluate ($data.nc3sym = $nc3sym) |
| evaluate ($data.ns3sym = $ns3sym) |
| evaluate ($data.nc4sym = $nc4sym) |
| evaluate ($data.nc5sym = $nc5sym) |
| evaluate ($data.nc6sym = $nc6sym) |
|
|
| !Electrostatics: |
| evaluate ($Data.flags.dihed =$dihedflag) |
| evaluate ($Data.flags.elec =$elecflag) |
| evaluate ($Data.epsilon =$epsilon) |
| evaluate ($Data.epsilon_cg =$epsilon_cg) |
| evaluate ($Data.dielec =$dielec) |
|
|
| !Interaction matrix: |
| evaluate ($nmol1=1) |
| while ($nmol1 <=$data.ncomponents) loop mol1 |
| evaluate ($nmol2=$nmol1 + 1) |
| evaluate ($scale.int_$nmol1_$nmol1 =$int_$nmol1_$nmol1) |
| while ($nmol2 <=$data.ncomponents) loop mol2 |
| evaluate ($scale.int_$nmol1_$nmol2 =$int_$nmol1_$nmol2) |
| evaluate ($scale.int_$nmol2_$nmol1 =$int_$nmol1_$nmol2) |
| evaluate ($nmol2=$nmol2 + 1) |
| end loop mol2 |
| evaluate ($nmol1 = $nmol1 + 1) |
| end loop mol1 |
|
|
|
|
| ! Unsupported restraints |
| evaluate ($Data.flags.em = false) |
| evaluate ($Data.flags.rg = false) |
| evaluate ($Data.flags.zres = false) |
| evaluate ($Data.flags.sani = false) |
| evaluate ($Data.flags.xrdc = false) |
| evaluate ($Data.flags.xpcs = false) |
| evaluate ($Data.flags.dani = false) |
| evaluate ($Data.flags.vean = false) |
|
|
| ! Other parameters |
| evaluate ($refine.keepwater = false) |
|
|
| !==================================================================! |
|
|
| evaluate ($whichMD="torsion") |
|
|
| {* Read paramters and set various force field related variables *} |
|
|
| @MODULE:read_param.cns |
| set seed $seed end |
|
|
| parameter |
| bond (resn WAT ) (resn WAT ) 1000 TOKEN |
| angle (resn WAT ) (resn WAT ) (resn WAT ) 500 TOKEN |
| bond (resn HOH ) (resn HOH ) 1000 TOKEN |
| angle (resn HOH ) (resn HOH ) (resn HOH ) 500 TOKEN |
| bond (resn TIP*) (resn TIP*) 1000 TOKEN |
| angle (resn TIP*) (resn TIP*) (resn TIP*) 500 TOKEN |
| end |
|
|
| {* Check for the presence of ions and add covalent bond *} |
|
|
| @MODULE:covalions.cns |
|
|
|
|
| {* Define various interaction and energetics settings *} |
|
|
| igroup |
| interaction (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) |
| (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1 end |
| interaction (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) |
| (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) weight * 1 vdw 0.0 elec 0.0 end |
| interaction (resn SHA) (not resn SHA) weight * 0 end |
| ! turn off vdw interaction of CG charged beads with all other particles |
| interaction (name SCD1) (all) weight vdw 0.0 end |
| interaction (name SCD2) (all) weight vdw 0.0 end |
| end |
|
|
| flag include bond angle impr vdw end |
|
|
| if ($Data.flags.dihed eq true) then |
| flag include dihed end |
| end if |
|
|
| if ($Data.flags.elec eq true) then |
| flag include elec end |
| if ($Data.dielec eq "rdie") then |
| parameter nbonds eps=$Data.epsilon rdie shift switch end end |
| ! shift statement needed first to activate switch (CNS bug?) |
| else |
| parameter nbonds eps=$Data.epsilon cdie end end |
| end if |
| else |
| evaluate ($elec=0.0) |
| flag exclude elec end |
| end if |
|
|
| ! check for the presence of a CG model |
| ! and adapt non-bonded parameters |
| do (store4 = 0) (all) |
| do (store4 = 1) (name BB or name BB#) |
| show sum (store4) (all) |
| if ($result > 0) then |
| parameter |
| nbonds |
| nbxmod=5 atom cdie shift |
| cutnb=15.0 ctofnb=14.0 ctonnb=12.0 eps=$Data.epsilon_cg e14fac=0.4 inhibit 0.25 |
| wmin=0.5 tolerance 0.5 |
| end |
| end |
| evaluate ($coarse = TRUE) |
| end if |
|
|
| parameter nbonds ? end end |
|
|
| do (fbeta=$Saprotocol.fbeta) (all) |
| do (mass=$Saprotocol.mass) (all) |
|
|
| !catch possible bound water and set high T steps to 0 |
| coor select ((resn WAT or resn HOH or resn TIP*)) end |
| if ($select gt 0) then |
| evaluate ($SaProtocol.initiosteps = 0) |
| evaluate ($SaProtocol.cool1_steps = 0) |
| evaluate ($refine.keepwater = true) |
| end if |
|
|
| ! random placement of molecules |
| if ($SaProtocol.separate eq true) then |
| @MODULE:separate.cns |
| end if |
| if ($SaProtocol.randrot eq true) then |
| @MODULE:random_rotations.cns |
| end if |
|
|
| {* Read the distance restraints ================================ *} |
| set seed $seed end |
| set message=normal echo=on end |
| inline @MODULE:read_data.cns |
|
|
| ! random removal of restaints |
| if ($Data.randremoval eq true) then |
| noe cv $npart ? end |
| end if |
|
|
| if ( $log_level = "verbose" ) then |
| set message=all echo=on end |
| elseif ( $log_level = "normal" ) then |
| set message=normal echo=off end |
| else |
| set message=off echo=off end |
| end if |
|
|
| evaluate ($numnoe = 0) |
|
|
| !Make sure that at least as many distance restraints are successfully |
| !read as the number of partitions for cross-validation |
| evaluate ($numnoe = 999) |
| noe ? end |
| if ($NUMNOE = 0) then |
| if ($Data.ncomponents > 1) then |
| if ($Data.contactairs eq FALSE) then |
| if ($Data.cmrest eq FALSE) then |
| evaluate ($errfile = "MODDIR:WARNING") |
| fileexist $errfile end |
| if ($result eq false) then |
| set display=$errfile end |
| display TOTAL NUMBER OF DISTANCE RESTRAINTS FOR FLEXIBLE REFINEMENT IS ZERO! |
| display CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS |
| close $errfile end |
| end if |
| end if |
| end if |
| end if |
| evaluate ($Data.npart = 1) |
| evaluate ($Data.randremoval = FALSE) |
| end if |
|
|
| if ($NUMNOE lt $Data.npart) then |
| noe part=1 end |
| evaluate ($Data.npart = 1) |
| evaluate ($Data.randremoval = FALSE) |
| end if |
|
|
|
|
| {* set the energy flags ======================================================== *} |
|
|
| inline @MODULE:setflags.cns |
|
|
| {* Check for other restraints ================================================== *} |
|
|
| @MODULE:symmultimer.cns |
|
|
| if ($Data.cmrest eq true ) then |
| @MODULE:cm-restraints.cns |
| end if |
|
|
| if ($Data.contactairs eq true ) then |
| @MODULE:contactairs.cns |
| end if |
|
|
| if ($Data.dnarest eq true ) then |
| @MODULE:dna-rna_restraints.cns |
| end if |
|
|
| if ($Data.ssdihed eq "all" ) then |
| inline @MODULE:protein-ss-restraints-all.cns |
| end if |
| if ($Data.ssdihed eq "alpha" ) then |
| inline @MODULE:protein-ss-restraints-alpha.cns |
| end if |
| if ($Data.ssdihed eq "alphabeta" ) then |
| inline @MODULE:protein-ss-restraints-alpha-beta.cns |
| end if |
|
|
| {* Check for the presence of ions and add distance restraints *} |
| @MODULE:restrain-ions.cns |
|
|
|
|
| {* Check first for failed structures =========================================== *} |
| evaluate ($failure = false) |
| evaluate ($filefail=$output_pdb_filename - ".pdb" + ".fail") |
| fileexist $filefail end |
| evaluate ($failure = $result) |
|
|
|
|
| {* Define initial weights for distance restraints ============================== *} |
| evaluate ($unambig_scale = $Data.unambig_hot) |
| evaluate ($ambig_scale = $Data.ambig_hot) |
| evaluate ($hbond_scale = $Data.hbond_hot) |
|
|
| noe |
| scale dist $unambig_scale |
| scale ambi $ambig_scale |
| scale hbon $hbond_scale |
| end |
|
|
| {* Stage 0 ================================== initial EM for flexible parts only *} |
|
|
| ! get initial energy |
| energy end |
|
|
| ! fix the residues describing the shape |
| fix sele=(resn SHA) end |
|
|
| ! define flexible interface |
| @MODULE:flex_segment_back.cns |
| fix sele=((attr store5 = 0 or name OO or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP*)) end |
|
|
| ! energy minimization |
| if ($nemsteps > 0) then |
| minimize powell nstep=$nemsteps drop=10.0 nprint=25 end |
| end if |
|
|
| fix sele=(not all) end |
|
|
| ! get initial energy |
| energy end |
|
|
| ! fix the residues describing the shape |
| fix sele=(resn SHA) end |
|
|
| ! the following is added to avoid the generation of the torsion angle topology if not needed |
| ! in cases where the number of steps is set to 0 (avoid issues with isolated atoms) |
| eval ($torsiondone = false) |
|
|
| ! start SA in torsion angle unless a failure was detected |
| if ($failure eq false) then |
|
|
| {* Stage 1 ======================================= rigid body high temperature search*} |
|
|
| if ($nfle > 0) then |
| ! reduce timestep in case of fully flexible segments |
| evaluate ($SaProtocol.tadfactor = min(4,$SaProtocol.tadfactor)) |
| end if |
| if ($SaProtocol.initiosteps > 0) then |
| inline @MODULE:flex_segment.cns |
| @MODULE:torsiontop.cns |
| eval ($torsiondone = true) |
| @MODULE:sa_ltad_hightemp.cns |
| end if |
|
|
| {* Stage 2 ======================================= rigid body first slow cooling *} |
|
|
| if ($SaProtocol.cool1_steps > 0) then |
| if ($torsiondone ne true) then |
| inline @MODULE:flex_segment.cns |
| @MODULE:torsiontop.cns |
| eval ($torsiondone = true) |
| end if |
| if ($nfle > 0) then |
| ! reduce timestep in case of fully flexible segments |
| evaluate ($SaProtocol.tadfactor = min(4,$SaProtocol.tadfactor)) |
| end if |
| @MODULE:sa_ltad_cool1.cns |
| end if |
|
|
| {* Stage 3 ======================================= second slow cooling *} |
| {* flexible side-chains and reduced time step *} |
|
|
| if ($SaProtocol.cool2_steps > 0) then |
| if ($torsiondone eq true) then |
| dyna tors topo reset end end |
| end if |
| inline @MODULE:flex_segment_side.cns |
| @MODULE:torsiontop.cns |
| eval ($torsiondone = true) |
| evaluate ($SaProtocol.tadfactor = 1) |
| @MODULE:sa_ltad_cool2.cns |
| end if |
|
|
| {* Stage 4 ============================================ third slow cooling *} |
| {* flexible side-chains and backbone at interface and reduced time step *} |
|
|
| if ($SaProtocol.cool3_steps > 0) then |
| if ($torsiondone eq true) then |
| dyna tors topo reset end end |
| end if |
| inline @MODULE:flex_segment_back.cns |
| @MODULE:torsiontop.cns |
| eval ($torsiondone = true) |
| evaluate ($SaProtocol.tadfactor = 1) |
| @MODULE:sa_ltad_cool3.cns |
| end if |
|
|
| end if |
|
|
| {* Stage 5 =========================== final minimization *} |
|
|
| ! define flexible segments and fix the remaining of the structure |
| @MODULE:flex_segment_back.cns |
| fix sele=((attr store5 = 0 or name OO or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP* or resn XAN)) end |
|
|
| ! energy minimization |
| if ($nemsteps > 0) then |
| minimize powell nstep=$nemsteps drop=10.0 nprint=25 end |
| end if |
|
|
| ! final energy |
| fix sele=(not all) end |
|
|
| {* ======================= calculate free molecules internal energy *} |
|
|
| igroup |
| interaction (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) |
| (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) weight * 1 end |
| end |
|
|
| do (refx=x) (all) |
| do (refy=y) (all) |
| do (refz=z) (all) |
|
|
| fix sele=(resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DMS) end |
|
|
| flag excl noe dani sani vean xrdc xpcs coll cdih zhar end |
| flag include bond angle dihe impr vdw end |
|
|
| evaluate ($elec = 0.0) |
| evaluate ($eintfree = 0.0) |
| if ($Data.flags.elec eq true) then |
| flag include elec end |
| end if |
|
|
| if ($Data.dielec eq "rdie") then |
| parameter nbonds eps=$Data.epsilon rdie shift switch end end |
| ! shift statement needed first to activate switch (CNS bug?) |
| else |
| parameter nbonds eps=$Data.epsilon cdie end end |
| end if |
| parameter nbonds ? end end |
| inline @MODULE:calc_free-ene.cns |
|
|
| fix sele=(not all) end |
|
|
| do (x = refx) (all) |
| do (y = refy) (all) |
| do (z = refz) (all) |
|
|
|
|
| {* ===================== calculate complex internal energy *} |
|
|
| evaluate ($kinter = 1.0) |
| flag include bond angle dihe impr vdw end |
| energy end |
|
|
| @MODULE:scale_intra_only.cns |
|
|
| evaluate ($elec = 0.0) |
| evaluate ($eintcplx = 0.0) |
| if ($Data.flags.elec eq true) then |
| flag include elec end |
| end if |
|
|
| energy end |
|
|
| evaluate ($eintcplx = $bond + $angl + $impr + $dihe + $vdw + $elec) |
| evaluate ($ebond = $bond) |
| evaluate ($eangl= $angl) |
| evaluate ($eimpr= $impr) |
| evaluate ($edihe= $dihe) |
|
|
| evaluate ($result=0) |
| print thres=0.05 bonds |
| evaluate ($rms_bonds=$result) |
| evaluate ($result=0) |
| print thres=5. angles |
| evaluate ($rms_angles=$result) |
| evaluate ($result=0) |
| print thres=5. impropers |
| evaluate ($rms_impropers=$result) |
| evaluate ($result=0) |
| print thres=30. dihedrals |
| evaluate ($rms_dihedrals=$result) |
|
|
|
|
| {* ===================== calculate final energies and write structure *} |
| evaluate ($cdih=0.0) |
| flag incl noe cdih end |
| if ($Data.ncomponents > 1) then |
| evaluate ($kinter = 1.0) |
| @MODULE:scale_inter_final.cns |
| else |
| @MODULE:scale_intra_only.cns |
| end if |
|
|
| noe |
| scale dist $Data.unambig_cool3 |
| scale ambi $Data.ambig_cool3 |
| scale hbon $Data.hbond_cool3 |
| scale symm 0.0 |
| scale cont 0.0 |
| end |
| energy end |
| evaluate ($eair= $noe) |
|
|
| evaluate ($esym = 0.0) |
| evaluate ($ncs = 0.0) |
| evaluate ($zhar = 0.0) |
| evaluate ($rms_test_noe = 0.0) |
| evaluate ($violations_test_noe = 0) |
| if ($Data.flags.sym eq true) then |
| ! calculatee first the symmetry energy |
| noe reset nres= 1200000 end |
| @MODULE:symmultimer.cns |
| noe |
| scale symm $Data.ksym |
| end |
| energy end |
| evaluate ($esym = $noe) |
| noe reset end |
| set seed=$seed end |
| !read back all the distance restraints: |
| @@MODULE:read_noes.cns |
| ! random removal of restaints |
| if ($Data.randremoval eq true) then |
| noe cv $npart ? end |
| end if |
| noe |
| scale dist $Data.unambig_cool3 |
| scale ambi $Data.ambig_cool3 |
| scale hbon $Data.hbond_cool3 |
| end |
| evaluate ($result = 0) |
| print threshold=0.3 noe |
| evaluate ($rms_noe=$result) |
| evaluate ($violations_noe=$violations) |
| if ($Data.randremoval eq true) then |
| evaluate ($rms_test_noe=$test_rms) |
| evaluate ($violations_test_noe=$test_violations) |
| end if |
| else |
| evaluate ($result = 0) |
| print threshold=0.3 noe |
| evaluate ($rms_noe=$result) |
| evaluate ($violations_noe=$violations) |
| if ($Data.randremoval eq true) then |
| evaluate ($rms_test_noe=$test_rms) |
| evaluate ($violations_test_noe=$test_violations) |
| end if |
| end if |
|
|
| if ($Data.dnarest eq true ) then |
| @MODULE:dna-rna_restraints.cns |
| end if |
|
|
| energy end |
| evaluate ($etot = $ener - $noe) |
| evaluate ($noe = $eair) |
| evaluate ($etot = $etot + $noe) |
|
|
| inline @MODULE:print_coorheader.cns |
|
|
|
|
| {* determine whether the final models should be reoriented along their principal *} |
| {* axes before writing to file ================================================= *} |
| eval($reorient = true) |
| evaluate ($ncount = 0) |
| while ($ncount < $data.ncomponents) loop orientmol |
| evaluate ($ncount = $ncount + 1) |
| eval($watersegname_$ncount="WA" + encode($ncount)) |
| if ($mol_fix_origin_$ncount eq true) then |
| eval($reorient = false) |
| end if |
| end loop orientmol |
|
|
| if ($reorient = true) then |
| coor sele= (not name H* and not resn ANI and not resn XAN and not resn DAN) orient end |
| end if |
|
|
| inline @MODULE:check_coordinates.cns |
| |
| if ($failure eq true) then |
| evaluate ($failfile = $output_pdb_filename - ".pdb" + ".fail") |
| set display=$failfile end |
| display "MAX/MIN possible coordinates exceeded - stopping" |
| close $failfile end |
| stop |
| else |
| write coordinates format=pdbo output=$output_pdb_filename end |
| end if |
|
|
| display OUTPUT: $output_pdb_filename |
|
|
| stop |
|
|
