Hi all I just found a solution, after playing around with CIF the issue appears to be a missing value-string after:
data_ however making it data_X - X being any string after, everything works well ie saving as CIF in COOT > phenix.refine After adding the string there, phenix.refine can refine and outputs another CIF. This CIF when opened and saved again in COOT outputs a string after data_X Seeing all of that, the easiest way to avoid any of this is to open directly in COOT a valid CIF (not PDB), before saving again as a CIF or else it might cause problems with phenix.refine. -- Kelvin Lau https://people.epfl.ch/kelvin.lau <https://people.epfl.ch/kelvin.lau> Scientist - Protein production and structure core facility – PTPSP Co-President – EPFL Scientific Staff Association – ELSA EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch <mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267 <tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494 <tel:+41%2021%2069%C2%A030267> On 21.02.2025, 15:28, "Mailing list for users of COOT Crystallographic Software on behalf of Kelvin Lau" <COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> on behalf of 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk <mailto:00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>> wrote: 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 # ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/> ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
