Hi Sampath
Make sure that the files that you have generated from the mtz files have the
header set according to what CNS needs.
Here it seems that the .cv file does not have the required header.
If u generate a .cv file using another program... say XDS, then you will see
that the top of the .cv file has a header like the following.
NREFlection= 24277
ANOMalous=FALSe
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
The NREFLECTION is the number of reflections in your data file.
It is here in the header that it declares FOBS and the data type, etc. CNS
must have this header in order to decipher the columns and proceed.
I have often seen that converting from MTZ to CNS format results in a file
with a missing header. I generally generate the header and put it in myself.
Hope this helps.
Regards.
Avinash.
*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,
Avinash Gill
Graduate Student
Dartmouth Medical School
Biochemistry Dept
HB 7200 Vail Bldg
Hanover NH 03755
*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,
On 7/16/07, Sampath Natarajan <[log in to unmask]> wrote:
>
> Dear all,
>
> I have a problem while running CNS minimize refinement. I have created the
> hkl file from mtz using CCP4. From this hkl file I've created the *.cv,
> *.mtf and *.pdb files.
>
> After running the CNS minimize refinement, the program was aborted and an
> error message was displayed as :
>
> "Error: required observed amplitude array "fobs" does not exist"
>
> I don't know where the problem is. If anyone knows, it would be of great
> help. For more information, I've given the log file (which I got after CNS
> minimize refinement) at the bottom of this mail.
>
>
> *Log file:*
>
> FFT3C: Using FFTPACK4.1
> 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> @@¶meter_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> @@¶meter_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 $VDW_EPS set to 0.100000 (real)
> PARRDR>
> PARRDR> end if
> PARRDR> if ( &BLANK%parameter_infile_3 = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@¶meter_infile_3
> ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/ion.param
> opened.
> PARRDR>remarks file toppar/ion.param
> PARRDR>remarks nonbonded parameters for common ions
> PARRDR>remarks new parameters derived from literature for single atom
> species
> PARRDR>remarks PDA 02/09/99
> PARRDR>
> PARRDR>set echo=off end
> Program version= 1.1 File version= 1.1
> PARRDR> end if
> PARRDR> if ( &BLANK%parameter_infile_4 = false ) then
> NEXTCD: condition evaluated as false
> PARRDR> @@¶meter_infile_4
> PARRDR> end if
> PARRDR> if ( &BLANK%parameter_infile_5 = false ) then
> NEXTCD: condition evaluated as false
> PARRDR> @@¶meter_infile_5
> PARRDR> end if
> PARRDR> end
> CNSsolve>
> CNSsolve> xray
> XRAY>
> XRAY> @CNS_XTALLIB:spacegroup.lib (sg=&sg;
> ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/xtal/spacegroup.lib
> opened.
> XRAY>! file libraries/xtal/spacegroup.lib
> XRAY>! library of symmetry operators for CNS
> XRAY>! Automatically generated with SgInfo Version 2.00a13
> XRAY>
> XRAY>module
> MODULE-DECLARATION>(
> MODULE-DECLARATION> &sg=$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
> **************************************************************
> Error: required observed amplitude array "fobs" does not exist
> **************************************************************
> % error encountered: ABORT statement specified.
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
>
>
> *************************************************
> **Dr. N.SAMPATH
> **Post Doctoral Fellow*
> *Department of Molecular & Cell Biology
> **Samsung Biomedical Research Institute
> Sungkyunkwan Univ. School of Medicine
> Suwon 440-746, S.Korea
> **************************************************
> tel : 82-31-299-6150 &** 82-31-299-6155
> *************************************************
>
> ------------------------------
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