Hello,

As I require using 5-letter ligand codes, I am modelling within Coot 0.9.8.94 
EL, saving as a CIF (as PDB format truncates 5>3 letters).

After that I am trying to open the file within phenix.refine. I get an error as 
such

File format error:
X.CIF (line 1): error 4 : Unexpected token, at offset 0 near loop_ :
unexpected input... expected one of : Unable to process inputs

I tried to find what this error is but I keep on getting it no matter what 
lines I delete.

The beginning of my CIF is below

Any ideas on getting CIF outputs from COOT to open in phenix.refine?

Best

Kelvin
______
>First few lines of my CIF saved directly from Coot 0.9.8.94 EL

data_

_database.entry_id      ?
_database.code_NDB      ?
_database.code_PDB      ?
_database.date_original ?

_struct_keywords.ndb_keywords ?

_refine.ls_d_res_high ?

loop_
_ndb_database_remark.id
_ndb_database_remark.text
 3 " "
 3 REFINEMENT.
 3 "  PROGRAM     : PHENIX (???)"
 3 "  AUTHORS     : Adams,Afonine,Bunkoczi,Burnley,Chen,Dar,Davis,"
 3 "              : Draizen,Echols,Gildea,Gros,Grosse-Kunstleve,Headd,"
 3 "              : Hintze,Hung,Ioerger,Liebschner,McCoy,McKee,Moriarty,"
 3 "              : Oeffner,Poon,Read,Richardson,Richardson,Sacchettini,"
 3 "              : Sauter,Sobolev,Storoni,Terwilliger,Williams,Zwart"
 3 " "
 3 " X-RAY DATA."
 3 " "
 3 " REFINEMENT TARGET : ML"
 3 " "
 3 " DATA USED IN REFINEMENT."
 3 "  RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33"
 3 "  RESOLUTION RANGE LOW  (ANGSTROMS) : 19.47"
 3 "  MIN(FOBS/SIGMA_FOBS)              : 1.34"
 3 "  COMPLETENESS FOR RANGE        (%) : 99.83"
 3 "  NUMBER OF REFLECTIONS             : 19797"
 3 "  NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 19797"
 3 " "
 3 " FIT TO DATA USED IN REFINEMENT."
 3 "  R VALUE     (WORKING + TEST SET) : 0.2157"
 3 "  R VALUE            (WORKING SET) : 0.2138"
 3 "  FREE R VALUE                     : 0.2525"
 3 "  FREE R VALUE TEST SET SIZE   (%) : 4.80"
 3 "  FREE R VALUE TEST SET COUNT      : 950"
 3 " "
 3 " FIT TO DATA USED IN REFINEMENT (IN BINS)."
 3 "  BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE  CCWOR"
 3 "    1   19.47 -    4.45    1.00     2803   130  0.1757 0.1944   0.92"
 3 "    2    4.45 -    3.54    1.00     2715   136  0.1815 0.2027   0.91"
 3 "    3    3.54 -    3.09    1.00     2711   132  0.2307 0.2887   0.85"
 3 "    4    3.09 -    2.81    1.00     2663   138  0.2539 0.2819   0.82"
 3 "    5    2.81 -    2.61    1.00     2672   124  0.2661 0.3420   0.81"
 3 "    6    2.61 -    2.46    1.00     2656   146  0.2646 0.3607   0.82"
 3 "    7    2.46 -    2.33    0.99     2627   144  0.2496 0.3099   0.83"
 3 " "
 3 " BULK SOLVENT MODELLING."
 3 "  METHOD USED        : FLAT BULK SOLVENT MODEL"
 3 "  SOLVENT RADIUS     : 1.10"
 3 "  SHRINKAGE RADIUS   : 0.90"
 3 "  GRID STEP          : 0.60"
 3 " "
 3 " ERROR ESTIMATES."
 3 "  COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.33"
 3 "  PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.46"
 3 " "
 3 " STRUCTURE FACTORS CALCULATION ALGORITHM : FFT"
 3 " "
 3 " B VALUES."
 3 "  FROM WILSON PLOT           (A**2) : 33.77"
 3 "  Individual atomic B"
 3 "                 min    max   mean <Bi,j>   iso aniso"
 3 "    Overall:   14.91  79.20  32.24   4.79  2182     0"
 3 "    Protein:   14.91  79.20  32.24   4.79  2182     0"
 3 "    Chain  A:  14.91  79.20  32.24    N/A  2182     0"
 3 "    Histogram:"
 3 "        Values      Number of atoms"
 3 "     14.91 - 21.34        93"
 3 "     21.34 - 27.77       605"
 3 "     27.77 - 34.20       769"
 3 "     34.20 - 40.63       433"
 3 "     40.63 - 47.05       161"
 3 "     47.05 - 53.48        76"
 3 "     53.48 - 59.91        26"
 3 "     59.91 - 66.34        12"
 3 "     66.34 - 72.77         3"
 3 "     72.77 - 79.20         4"
 3 " REMARK   3"
 3 " GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2"
 3 " DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES."
 3 "   BOND      :  0.011   0.095   2235  Z= 0.508"
 3 "   ANGLE     :  1.085   6.025   3045  Z= 0.625"
 3 "   CHIRALITY :  0.062   0.187    326"
 3 "   PLANARITY :  0.012   0.096    402"
 3 "   DIHEDRAL  : 15.617 154.000    792"
 3 "   MIN NONBONDED DISTANCE : 2.455"
 3 " REMARK   3"
 3 " MOLPROBITY STATISTICS."
 3 "   ALL-ATOM CLASHSCORE : 3.29"
 3 "   RAMACHANDRAN PLOT:"
 3 "     OUTLIERS :  0.00 %"
 3 "     ALLOWED  :  2.84 %"
 3 "     FAVORED  : 97.16 %"
 3 "   ROTAMER:"
 3 "     OUTLIERS :  0.00 %"
 3 "     ALLOWED  : 10.04 %"
 3 "     FAVORED  : 89.96 %"
 3 "   CBETA DEVIATIONS :  0.00 %"
 3 "   PEPTIDE PLANE:"
 3 "     CIS-PROLINE     : 0.00 %"
 3 "     CIS-GENERAL     : 0.00 %"
 3 "     TWISTED PROLINE : 0.00 %"
 3 "     TWISTED GENERAL : 0.00 %"
 3 " "
 3 " RAMA-Z (RAMACHANDRAN PLOT Z-SCORE):"
 3 " INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD"
 3 " SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY;"
 3 " THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER."
 3 "   WHOLE: -0.65 (0.46), RESIDUES: 282"
 3 "   HELIX:  NONE (NONE), RESIDUES: 0"
 3 "   SHEET:  0.48 (0.46), RESIDUES: 121"
 3 "   LOOP : -1.19 (0.43), RESIDUES: 161"
 3 " "
 3 " MAX DEVIATION FROM PLANES:"
 3 "    TYPE  MAXDEV  MEANDEV LINEINFILE"
 3 "  ARG   0.011   0.002   ARG A 507"
 3 "  TYR   0.036   0.006   TYR A 537"
 3 "  PHE   0.018   0.004   PHE A 577"
 3 "  TRP   0.019   0.006   TRP A 352"
 3 "  HIS   0.008   0.003   HIS A 552"
 3 " "
#

loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_auth_atom_id
_struct_conn.pdbx_ptnr1_auth_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.ptnr2_auth_atom_id
_struct_conn.pdbx_ptnr2_auth_alt_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_symmetry
_struct_conn.link_dist
 1 LINK " N  " . ASN A 700 . " C  " . YXCVB A 701 . 1555 1555 -1
#

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