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CNSsolve>{+ file: minimize.inp +}
CNSsolve>{+ directory: xtal_refine +}
CNSsolve>{+ description: Crystallographic conjugate gradient minimization refinement +}
CNSsolve>{+ authors: Axel T. Brunger, and Paul D. Adams +}
CNSsolve>{+ copyright: Yale University +}
CNSsolve>
CNSsolve>{+ reference: A.T. Brunger, The Free R Value: a Novel Statistical
CNSsolve>              Quantity for Assessing the Accuracy of Crystal Structures,
CNSsolve>              Nature 355, 472-474 (1992) +}
CNSsolve>{+ reference: N.S. Pannu and R.J. Read, Improved structure refinement
CNSsolve>              through maximum likelihood, Acta Cryst. A52, 659-668 (1996) +}
CNSsolve>{+ reference: P.D. Adams, N.S. Pannu, R.J. Read and A.T. Brunger,
CNSsolve>              Cross-validated Maximum Likelihood Enhances Crystallographic
CNSsolve>              Simulated Annealing Refinement, Proc. Natl. Acad. Sci. USA
CNSsolve>              94, 5018-5023 (1997) +}
CNSsolve>
CNSsolve>{- Guidelines for using this file:
CNSsolve>   - all strings must be quoted by double-quotes
CNSsolve>   - logical variables (true/false) are not quoted
CNSsolve>   - do not remove any evaluate statements from the file
CNSsolve>   - the selections store1 through store8 are available for general use -}
CNSsolve>
CNSsolve>{- begin block parameter definition -} define(
DEFINE>
DEFINE>{======================= molecular structure =========================}
DEFINE>
DEFINE>{* molecular topology file *}
DEFINE>{===>} structure_infile="2F_gen.mtf";
DEFINE>
DEFINE>{* parameter files *}
DEFINE>{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
DEFINE>{===>} parameter_infile_2="CNS_TOPPAR:water_rep.param";
DEFINE>{===>} parameter_infile_3="CNS_TOPPAR:ion.param";
DEFINE>{===>} parameter_infile_4="";
DEFINE>{===>} parameter_infile_5="";
DEFINE>
DEFINE>{* coordinate file *}
DEFINE>{===>} coordinate_infile="2F_gen.pdb";
DEFINE>
DEFINE>{====================== crystallographic data ========================}
DEFINE>
DEFINE>{* space group *}
DEFINE>{* use International Table conventions with subscripts substituted
DEFINE>   by parenthesis *}
DEFINE>{===>} sg="P3(1)21";
DEFINE>
DEFINE>{* unit cell parameters in Angstroms and degrees *}
DEFINE>{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
DEFINE>{===>} a=88.563;
DEFINE>{===>} b=88.563;
DEFINE>{===>} c=103.818;
DEFINE>{===>} alpha=90;
DEFINE>{===>} beta=90;
DEFINE>{===>} gamma=120;
DEFINE>
DEFINE>{* anomalous f' f'' library file *}
DEFINE>{* If a file is not specified, no anomalous contribution will be included *}
DEFINE>{+ choice: "CNS_XRAYLIB:anom_cu.lib" "CNS_XRAYLIB:anom_mo.lib" "" user_file +}
DEFINE>{===>} anom_library="";
DEFINE>
DEFINE>{* reflection files *}
DEFINE>{* specify non-anomalous reflection files before anomalous reflection files. *}
DEFINE>{* files must contain unique array names otherwise errors will occur *}
DEFINE>{===>} reflection_infile_1="2F.cv";
DEFINE>{===>} reflection_infile_2="";
DEFINE>{===>} reflection_infile_3="";
DEFINE>
DEFINE>{* reciprocal space array containing observed amplitudes: required *}
DEFINE>{===>} obs_f="fobs";
DEFINE>
DEFINE>{* reciprocal space array containing sigma values for amplitudes: required *}
DEFINE>{===>} obs_sigf="sigma";
DEFINE>
DEFINE>{* reciprocal space array containing test set for cross-validation: required *}
DEFINE>{* cross-validation should always be used, with the possible exception
DEFINE>   of a final round of refinement including all data *}
DEFINE>{* cross-validation is always required for the maximum likelihood targets *}
DEFINE>{===>} test_set="test";
DEFINE>
DEFINE>{* number for selection of test reflections: required for cross-validation *}
DEFINE>{* ie. reflections with the test set array equal to this number will be
DEFINE>       used for cross-validation, all other reflections form the working set *}
DEFINE>{===>} test_flag=1;
DEFINE>
DEFINE>{* reciprocal space array containing weighting scheme for observed
DEFINE>   amplitudes: optional *}
DEFINE>{* only used for the "residual" and "vector" targets - this will
DEFINE>   default to a constant value of 1 if array is not present *}
DEFINE>{===>} obs_w="";
DEFINE>
DEFINE>{* reciprocal space array containing observed intensities: optional *}
DEFINE>{* required for the "mli" target *}
DEFINE>{===>} obs_i="";
DEFINE>
DEFINE>{* reciprocal space array containing sigma values for intensities: optional *}
DEFINE>{* required for the "mli" target *}
DEFINE>{===>} obs_sigi="";
DEFINE>
DEFINE>{* reciprocal space arrays with experimental phase probability
DEFINE>   distribution: optional *}
DEFINE>{* Hendrickson-Lattman coefficients A,B,C,D *}
DEFINE>{* required for the "mlhl" target *}
DEFINE>{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
DEFINE>{===>} obs_pa="";
DEFINE>{===>} obs_pb="";
DEFINE>{===>} obs_pc="";
DEFINE>{===>} obs_pd="";
DEFINE>
DEFINE>{* complex reciprocal space array containing experimental phases: optional *}
DEFINE>{* required for the "mixed" and "vector" targets *}
DEFINE>{===>} obs_phase="";
DEFINE>
DEFINE>{* reciprocal space array containing experimental figures of merit: optional *}
DEFINE>{* required for the "mixed" target *}
DEFINE>{===>} obs_fom="";
DEFINE>
DEFINE>{* resolution limits to be used in refinement *}
DEFINE>{* the full resolution range of observed data should be used in refinement.
DEFINE>   A bulk solvent correction should be applied to allow the use of low
DEFINE>   resolution terms. If no bulk solvent correction is applied, data must
DEFINE>   be truncated at a lower resolution limit of between 8 and 6 Angstrom. *}
DEFINE>{+ table: rows=1 "resolution" cols=2 "lowest" "highest" +}
DEFINE>{===>} low_res=30.0;
DEFINE>{===>} high_res=2.5;
DEFINE>
DEFINE>{* apply rejection criteria to amplitudes or intensities *}
DEFINE>{+ choice: "amplitude" "intensity" +}
DEFINE>{===>} obs_type="amplitude";
DEFINE>
DEFINE>{* Observed data cutoff criteria: applied to amplitudes or intensities *}
DEFINE>{* reflections with magnitude(Obs)/sigma < cutoff are rejected. *}
DEFINE>{===>} sigma_cut=0.0;
DEFINE>
DEFINE>{* rms outlier cutoff: applied to amplitudes or intensities *}
DEFINE>{* reflections with magnitude(Obs) > cutoff*rms(Obs) will be rejected *}
DEFINE>{===>} obs_rms=10000;
DEFINE>
DEFINE>{=================== non-crystallographic symmetry ===================}
DEFINE>
DEFINE>{* NCS-restraints/constraints file *}
DEFINE>{* see auxiliary/ncs.def *}
DEFINE>{===>} ncs_infile="";
DEFINE>
DEFINE>{============ initial B-factor and bulk solvent corrections ==========}
DEFINE>
DEFINE>{* initial B-factor correction *}
DEFINE>{+ choice: "no" "isotropic" "anisotropic" "anisotropic_fixed_isotropic" +}
DEFINE>{===>} bscale="anisotropic";
DEFINE>
DEFINE>{* lower resolution limit for B-factor correction *}
DEFINE>{* the correction can only be calculated using data truncated at a
DEFINE>   lower resolution limit of between 8 and 6 A. The correction will be
DEFINE>   applied to all reflections *}
DEFINE>{===>} low_res_bscale=6.0;
DEFINE>
DEFINE>{* bulk solvent correction *}
DEFINE>{* a mask is required around the molecule(s). The region
DEFINE>   outside this mask is the solvent region *}
DEFINE>{+ choice: true false +}
DEFINE>{===>} bulk_sol=true;
DEFINE>
DEFINE>{* bulk solvent mask file *}
DEFINE>{* mask will be read from O type mask file if a name is given
DEFINE>   otherwise calculated from coordinates of selected atoms *}
DEFINE>{===>} bulk_mask_infile="";
DEFINE>
DEFINE>{* solvent density level *}
DEFINE>{* if negative, determined automatically
DEFINE>   if positive, fixed at value given *}
DEFINE>{===>} sol_k=-1;
DEFINE>
DEFINE>{* solvent B-factor *}
DEFINE>{* if negative, determined automatically
DEFINE>   if positive, fixed at value given *}
DEFINE>{===>} sol_b=-1;
DEFINE>
DEFINE>{========================== atom selection ===========================}
DEFINE>
DEFINE>{* select atoms to be included in refinement *}
DEFINE>{* this should include all conformations if multiple conformations are used *}
DEFINE>{===>} atom_select=(known and not hydrogen);
DEFINE>
DEFINE>{* select fixed atoms *}
DEFINE>{* note: atoms at special positions are automatically fixed. So,
DEFINE>   you don't have to explicitly fix them here. *}
DEFINE>{===>} atom_fixed=(none);
DEFINE>
DEFINE>{* select atoms to be harmonically restrained during refinement *}
DEFINE>{===>} atom_harm=(none);
DEFINE>
DEFINE>{* harmonic restraint constant - for harmonically restrained atoms *}
DEFINE>{===>} k_harmonic=10;
DEFINE>
DEFINE>{* select atoms in alternate conformation 1 *}
DEFINE>{===>} conf_1=(none);
DEFINE>
DEFINE>{* select atoms in alternate conformation 2 *}
DEFINE>{===>} conf_2=(none);
DEFINE>
DEFINE>{* select atoms in alternate conformation 3 *}
DEFINE>{===>} conf_3=(none);
DEFINE>
DEFINE>{* select atoms in alternate conformation 4 *}
DEFINE>{===>} conf_4=(none);
DEFINE>
DEFINE>{* additional restraints file *}
DEFINE>{* eg. auxiliary/dna-rna_restraints.def *}
DEFINE>{===>} restraints_infile="";
DEFINE>
DEFINE>{===================== minimization parameters =======================}
DEFINE>
DEFINE>{* number of minimization steps *}
DEFINE>{===>} minimize_nstep=100;
DEFINE>
DEFINE>{* number of cycles *}
DEFINE>{===>} num_cycles=1;
DEFINE>
DEFINE>{* refinement target *}
DEFINE>{+ list: mlf: maximum likelihood target using amplitudes
DEFINE>         mli: maximum likelihood target using intensities
DEFINE>        mlhl: maximum likelihood target using amplitudes
DEFINE>              and phase probability distribution
DEFINE>    residual: standard crystallographic residual
DEFINE>      vector: vector residual
DEFINE>       mixed: (1-fom)*residual + fom*vector
DEFINE>        e2e2: correlation coefficient using normalized E^2
DEFINE>        e1e1: correlation coefficient using normalized E
DEFINE>        f2f2: correlation coefficient using F^2
DEFINE>        f1f1: correlation coefficient using F +}
DEFINE>{+ choice: "mlf" "mli" "mlhl" "residual" "vector" "mixed"
DEFINE>           "e2e2" "e1e1" "f2f2" "f1f1" +}
DEFINE>{===>} reftarget="mlf";
DEFINE>
DEFINE>{* Wa weight for X-ray term *}
DEFINE>{* this will be determined automatically if a negative value is given.
DEFINE>   Note: wa can be very different depending on the target - if it is not
DEFINE>         determined automatically make sure an appropriate value is used *}
DEFINE>{===>} wa=-1;
DEFINE>
DEFINE>{* number of bins for refinement target *}
DEFINE>{* this will be determined automatically if a negative value is given
DEFINE>   otherwise the specified number of bins will be used *}
DEFINE>{===>} target_bins=-1;
DEFINE>
DEFINE>{* memory allocation for FFT calculation *}
DEFINE>{* this will be determined automatically if a negative value is given
DEFINE>   otherwise the specified number of words will be allocated *}
DEFINE>{===>} fft_memory=-1;
DEFINE>
DEFINE>{=========================== output files ============================}
DEFINE>
DEFINE>{* output coordinate file *}
DEFINE>{===>} coordinate_outfile="2F_mini.pdb";
DEFINE>
DEFINE>{* format output coordinates for use in o *}
DEFINE>{* if false then the default CNS output coordinate format will be used *}
DEFINE>{+ choice: true false +}
DEFINE>{===>} pdb_o_format=true;
DEFINE>
DEFINE>{===========================================================================}
DEFINE>{        things below this line do not normally need to be changed          }
DEFINE>{===========================================================================}
DEFINE>
DEFINE> ) {- end block parameter definition -}
CNSsolve>
CNSsolve> checkversion 1.1
Program version= 1.1 File version= 1.1
CNSsolve>
CNSsolve> evaluate ($log_level=quiet)
Assuming literal string "QUIET"
EVALUATE: symbol $LOG_LEVEL set to "QUIET" (string)
CNSsolve>
CNSsolve> structure @&structure_infile end
ASSFIL: file 2F_gen.mtf opened.
STRUcture>data_cns_mtf
REMARKS FILENAME="2F_gen.mtf"
REMARKS coordinates built for atom: A    ILE 10   CD
REMARKS coordinates built for atom: A    ILE 19   CD
REMARKS coordinates built for atom: A    ILE 23   CD
REMARKS coordinates built for atom: A    ILE 57   CD
REMARKS coordinates built for atom: A    ILE 67   CD
REMARKS coordinates built for atom: A    ILE 72   CD
REMARKS coordinates built for atom: A    ILE 82   CD
REMARKS coordinates built for atom: A    ILE 134 CD
REMARKS coordinates built for atom: A    ILE 145 CD
REMARKS coordinates built for atom: A    ILE 149 CD
REMARKS coordinates built for atom: A    ILE 171 CD
REMARKS coordinates built for atom: A    ILE 219 CD
REMARKS coordinates built for atom: A    ILE 246 CD
REMARKS coordinates built for atom: A    ILE 261 CD
REMARKS coordinates built for atom: A    ILE 275 CD
REMARKS coordinates built for atom: A    ILE 281 CD
REMARKS coordinates built for atom: A    MET 282 OT1
REMARKS coordinates built for atom: A    MET 282 OXT
REMARKS DATE:16-Jul-2007 01:06:21       created by user: sam
REMARKS VERSION:1.1
Status of internal molecular topology database:
-> NATOM=       2297(MAXA=       40000) NBOND=       2349(MAXB=       40000)
-> NTHETA=      3167(MAXT=       80000) NGRP=         283(MAXGRP=     40000)
-> NPHI=        1479(MAXP=       80000) NIMPHI=       989(MAXIMP=     40000)
-> NNB=            0(MAXNB=      40000)
STRUcture>
STRUcture> end
CNSsolve>
CNSsolve> coordinates @&coordinate_infile
ASSFIL: file 2F_gen.pdb opened.
COOR>REMARK FILENAME="2F_gen.pdb"
COOR>REMARK coordinates built for atom: A    ILE 10   CD
COOR>REMARK coordinates built for atom: A    ILE 19   CD
COOR>REMARK coordinates built for atom: A    ILE 23   CD
COOR>REMARK coordinates built for atom: A    ILE 57   CD
COOR>REMARK coordinates built for atom: A    ILE 67   CD
COOR>REMARK coordinates built for atom: A    ILE 72   CD
COOR>REMARK coordinates built for atom: A    ILE 82   CD
COOR>REMARK coordinates built for atom: A    ILE 134 CD
COOR>REMARK coordinates built for atom: A    ILE 145 CD
COOR>REMARK coordinates built for atom: A    ILE 149 CD
COOR>REMARK coordinates built for atom: A    ILE 171 CD
COOR>REMARK coordinates built for atom: A    ILE 219 CD
COOR>REMARK coordinates built for atom: A    ILE 246 CD
COOR>REMARK coordinates built for atom: A    ILE 261 CD
COOR>REMARK coordinates built for atom: A    ILE 275 CD
COOR>REMARK coordinates built for atom: A    ILE 281 CD
COOR>REMARK coordinates built for atom: A    MET 282 OT1
COOR>REMARK coordinates built for atom: A    MET 282 OXT
COOR>REMARK DATE:16-Jul-2007 01:06:22       created by user: sam
COOR>REMARK VERSION:1.1
COOR>ATOM      1 CB GLU A   2     -52.577 51.518   4.795 1.00 92.26      A
COOR>ATOM      2 CG GLU A   2     -53.454 50.561   3.987 1.00 92.53      A
CNSsolve>
CNSsolve> parameter
PARRDR>   if ( &BLANK%parameter_infile_1 = false ) then
NEXTCD: condition evaluated as true
PARRDR>      @@&parameter_infile_1
ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/protein_rep.param opened.
PARRDR>remarks file toppar/protein_rep.param
PARRDR>remarks   protein parameters for crystallographic structure determination
PARRDR>remarks   with "soft" (purely repulsive) van der Waals parameters.
PARRDR>remarks
PARRDR>remarks file toppar/protein_rep.param
PARRDR>remarks Parameter file including bond and angle parameters
PARRDR>remarks derived from Cambridge Data Base model structures
PARRDR>remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991).
PARRDR>remarks
PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function.
PARRDR>remarks Small dihedral angle energy constants set to uniform small value.
PARRDR>remarks All other dihedral and improper energy constants set to uniform
PARRDR>remarks large values.
PARRDR>remarks
PARRDR>remarks Warning: these parameters are not suitable for free MD simulations
PARRDR>remarks
PARRDR>
PARRDR>!
PARRDR>! References:
PARRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and
PARRDR>! Angle Parameters for X-ray Protein-Structure Refinement,
PARRDR>! Acta Cryst. A47, 392-400.
PARRDR>!
PARRDR>! Hendrickson W.A. and Konnert J.H. in "Computing in
PARRDR>! Crystallography" (ed.   R. Diamond, S. Ramaseshan
PARRDR>! and K. Venkatesan) (Bangalore, Indian Institute of
PARRDR>! Science, 1980) 13.01-13.23
PARRDR>!
PARRDR>
PARRDR>set echo=off message=off end
Program version= 1.1 File version= 1.1
PARRDR>   end if
PARRDR>   if ( &BLANK%parameter_infile_2 = false ) then
NEXTCD: condition evaluated as true
PARRDR>      @@&parameter_infile_2
ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/water_rep.param opened.
PARRDR>remarks file toppar/water.param
PARRDR>remarks   water parameters for structure determination
PARRDR>remarks
PARRDR>
PARRDR>set echo=false end
Program version= 1.1 File version= 1.1
EVALUATE: symbol $VDW_RADIUS_O set to    2.90000     (real)
EVALUATE: symbol $VDW_RADIUS_HH set to    1.60000     (real)
EVALUATE: symbol $VDW_RADIUS_O set to    2.58361     (real)
EVALUATE: symbol $VDW_RADIUS_HH set to    1.42544     (real)
EVALUATE: symbol $VDW_RADIUS14_O set to    2.31634     (real)
EVALUATE: symbol $VDW_RADIUS14_HH set to    1.15817     (real)
EVALUATE: symbol $VDW_EPS set to   0.100000     (real)
PARRDR>
PARRDR>   end if
PARRDR>   if ( &BLANK%parameter_infile_3 = false ) then
NEXTCD: condition evaluated as true
PARRDR>      @@&parameter_infile_3
ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/ion.param opened.
PARRDR>remarks file toppar/ion.param
PARRDR>remarks nonbonded parameters for common ions
PARRDR>remarks new parameters derived from literature for single atom species
PARRDR>remarks PDA 02/09/99
PARRDR>
PARRDR>set echo=off end
Program version= 1.1 File version= 1.1
PARRDR>   end if
PARRDR>   if ( &BLANK%parameter_infile_4 = false ) then
NEXTCD: condition evaluated as false
PARRDR>      @@&parameter_infile_4
PARRDR>   end if
PARRDR>   if ( &BLANK%parameter_infile_5 = false ) then
NEXTCD: condition evaluated as false
PARRDR>      @@&parameter_infile_5
PARRDR>   end if
PARRDR> end
CNSsolve>
CNSsolve> xray
XRAY>
XRAY>   @CNS_XTALLIB:spacegroup.lib (sg=&sg;
ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/xtal/spacegroup.lib opened.
XRAY>! file libraries/xtal/spacegroup.lib
XRAY>! library of symmetry operators for CNS
XRAY>! Automatically generated with SgInfo Version 2.00a13
XRAY>
XRAY>module
MODULE-DECLARATION>(
MODULE-DECLARATION> &sg=$sg;
MODULE-DECLARATION> &sgparam=$sgparam;
MODULE-DECLARATION>)
&_2_SG set to &_1_SG
MODULE-INVOCATION>                                sgparam=$sgparam;)
&_2_SGPARAM set to $_1_SGPARAM
XRAY>
XRAY>set message ? end
MESSage=NORM
XRAY>evaluate ($message_old=$result)
EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string)
XRAY>set echo ? end
ECHO=TRUE {ON}
XRAY>evaluate ($echo_old=$result)
EVALUATE: symbol $ECHO_OLD set to TRUE (logical)
XRAY>set echo=off message=off end
Program version= 1.1 File version= 1.1
SYMMETRY: found symmetry operators for space group "P3(1)21" in library
XRAY>
XRAY>
XRAY>   a=&a b=&b c=&c alpha=&alpha beta=&beta gamma=&gamma
XRAY>
XRAY>   @CNS_XRAYLIB:scatter.lib
ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/xray/scatter.lib opened.
XRAY>! file libraries/xray/scatter.lib
XRAY>! Atomic scattering factors without anomalous contribution
XRAY>! Library for CNS
XRAY>
XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
XRAY>
XRAY>!BEWARE:
XRAY>!(1) element Cf (Californium) has to be referred to as Cff
XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
XRAY>!(3) types of elements with ionic state (i.e., +/-) specifications have
XRAY>!    to be put in double quotes in selection statements.
XRAY>
XRAY>set message ? end
MESSage=NORM
XRAY>evaluate ($message_old_sclib=$result)
EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
XRAY>set echo ? end
ECHO=TRUE {ON}
XRAY>evaluate ($echo_old_sclib=$result)
EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
XRAY>set echo=off message=off end
Program version= 1.1 File version= 1.1
XRAY>
XRAY>   if ( &BLANK%reflection_infile_1 = false ) then
NEXTCD: condition evaluated as true
XRAY>     reflection @@&reflection_infile_1 end
ASSFIL: file 2F.cv opened.
REFLection> NREFlection=     16608
XRAY: increasing space allocation for up to   16608 reflections.
REFLection> ANOMalous=FALSe { equiv. to HERMitian=TRUE}
REFLection> DECLare NAME=FCALC                  DOMAin=RECIprocal   TYPE=COMP END
XDECLARE: Object FCALC has been declared.
REFLection> DECLare NAME=TEST                   DOMAin=RECIprocal   TYPE=INTE END
XDECLARE: Object TEST has been declared.
REFLection> INDE     0    0   12 FCALC=   361.600   180.000 TEST=         0
XSFAL: allocating space for complex reciprocal space object.
XSFAL: allocating space for integer reciprocal space object.
XRRR2:    16608 new h,k,l indices have been added.
XRAY>   end if
XRAY>   if ( &BLANK%reflection_infile_2 = false ) then
NEXTCD: condition evaluated as false
XRAY>     reflection @@&reflection_infile_2 end
XRAY>   end if
XRAY>   if ( &BLANK%reflection_infile_3 = false ) then
NEXTCD: condition evaluated as false
XRAY>     reflection @@&reflection_infile_3 end
XRAY>   end if
XRAY>
XRAY> end
CNSsolve>
CNSsolve> if ( &BLANK%anom_library = false ) then
NEXTCD: condition evaluated as false
CNSsolve>   @@&anom_library
CNSsolve> else
CNSsolve>   set echo=off end
ANOMalous=FALSe {OFF}
NEXTCD: condition evaluated as false
CNSsolve> end if
CNSsolve>
CNSsolve> {- copy define parameters of optional arrays into symbols so
CNSsolve>    we can redefine them -}
CNSsolve>
CNSsolve> evaluate ($obs_i=&obs_i)
EVALUATE: symbol $OBS_I set to "" (string)
CNSsolve> evaluate ($obs_sigi=&obs_sigi)
EVALUATE: symbol $OBS_SIGI set to "" (string)
CNSsolve> evaluate ($obs_w=&obs_w)
EVALUATE: symbol $OBS_W set to "" (string)
CNSsolve> xray
XRAY>   @@CNS_XTALMODULE:checkrefinput (
ASSFIL: file /usr/local/cns/cns_solve_1.1/modules/xtal/checkrefinput opened.
XRAY>! Module file: checkrefinput
XRAY>!
XRAY>! CNS module
XRAY>! **********
XRAY>!
XRAY>! Authors: Axel Brunger and Paul Adams
XRAY>!
XRAY>! copyright Yale University
XRAY>!
XRAY>! Function:
XRAY>!    Checks the required input reciprocal space arrays
XRAY>!
XRAY>! Requirements:
XRAY>!    Needs to be called within xray
XRAY>
XRAY>module {checkrefinput}
MODULE-DECLARATION>
MODULE-DECLARATION>(
MODULE-DECLARATION> &reftarget="residual"; {string}
MODULE-DECLARATION> &obs_f;                {reciprocal space array}
MODULE-DECLARATION> &obs_sigf;             {reciprocal space array}
MODULE-DECLARATION> &test_set;             {reciprocal space array}
MODULE-DECLARATION> &obs_pa;               {reciprocal space array}
MODULE-DECLARATION> &obs_pb;               {reciprocal space array}
MODULE-DECLARATION> &obs_pc;               {reciprocal space array}
MODULE-DECLARATION> &obs_pd;               {reciprocal space array}
MODULE-DECLARATION> &obs_phase;            {reciprocal space array}
MODULE-DECLARATION> &obs_fom;              {reciprocal space array}
MODULE-DECLARATION> &obs_w;                {reciprocal space array}
MODULE-DECLARATION> &obs_i;                {reciprocal space array}
MODULE-DECLARATION> &obs_sigi;             {reciprocal space array}
MODULE-DECLARATION>)
MODULE-INVOCATION>                                  reftarget=&reftarget;
&_2_REFTARGET set to &_1_REFTARGET
MODULE-INVOCATION>                                  obs_f=&obs_f;
&_2_OBS_F set to &_1_OBS_F
MODULE-INVOCATION>                                  obs_sigf=&obs_sigf;
&_2_OBS_SIGF set to &_1_OBS_SIGF
MODULE-INVOCATION>                                  test_set=&test_set;
&_2_TEST_SET set to &_1_TEST_SET
MODULE-INVOCATION>                                  obs_pa=&obs_pa;
&_2_OBS_PA set to &_1_OBS_PA
MODULE-INVOCATION>                                  obs_pb=&obs_pb;
&_2_OBS_PB set to &_1_OBS_PB
MODULE-INVOCATION>                                  obs_pc=&obs_pc;
&_2_OBS_PC set to &_1_OBS_PC
MODULE-INVOCATION>                                  obs_pd=&obs_pd;
&_2_OBS_PD set to &_1_OBS_PD
MODULE-INVOCATION>                                  obs_phase=&obs_phase;
&_2_OBS_PHASE set to &_1_OBS_PHASE
MODULE-INVOCATION>                                  obs_fom=&obs_fom;
&_2_OBS_FOM set to &_1_OBS_FOM
MODULE-INVOCATION>                                  obs_w=$obs_w;
&_2_OBS_W set to $_1_OBS_W
MODULE-INVOCATION>                                  obs_i=$obs_i;
&_2_OBS_I set to $_1_OBS_I
MODULE-INVOCATION>                                  obs_sigi=$obs_sigi;
&_2_OBS_SIGI set to $_1_OBS_SIGI
MODULE-INVOCATION>                                  )
XRAY>
XRAY>set message ? end
MESSage=NORM
XRAY>evaluate ($message_old_cri=$result)
EVALUATE: symbol $MESSAGE_OLD_CRI set to "NORM" (string)
XRAY>set echo ? end
ECHO=TRUE {ON}
XRAY>evaluate ($echo_old_cri=$result)
EVALUATE: symbol $ECHO_OLD_CRI set to TRUE (logical)
XRAY>if ( $log_level = verbose ) then
NEXTCD: condition evaluated as false
XRAY> set echo=on message=normal end
XRAY>else
XRAY> set echo=off message=off end
Program version= 1.1 File version= 1.1