Pat, The Coot I’m using (Version 1.0.0) retains all the REMARK, LINK, CRYST1, and SCALE lines of the input .pdb file, as shown below. Is that what you mean by “refinement info”. BTW, for deposition I use PDB Extract (https://pdb-extract.wwpdb.org/) to combine .pdb file from phenix.refine, .log file from phenix.refine, Fobs .mtz file, and the aimless.log file into coordinate and structure factor cif files. PDB deposition with those two .cif files goes smoothly. Jack REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : Adams,Afonine,Bunkoczi,Burnley,Chen,Dar,Davis, REMARK 3 : Draizen,Echols,Gildea,Gros,Grosse-Kunstleve,Headd, REMARK 3 : Hintze,Hung,Ioerger,Liebschner,McCoy,McKee,Moriarty, REMARK 3 : Oeffner,Poon,Read,Richardson,Richardson,Sacchettini, REMARK 3 : Sauter,Sobolev,Storoni,Terwilliger,Williams,Zwart REMARK 3 REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.31 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.34 REMARK 3 NUMBER OF REFLECTIONS : 532934 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 279452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1859 REMARK 3 R VALUE (WORKING SET) : 0.1845 REMARK 3 FREE R VALUE : 0.2123 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 FREE R VALUE TEST SET COUNT : 26580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE CCWOR REMARK 3 1 97.45 - 5.22 0.96 17012 835 0.1455 0.1603 0.94 REMARK 3 2 5.22 - 4.14 0.91 16171 830 0.1273 0.1507 0.95 REMARK 3 3 4.14 - 3.62 0.93 16465 850 0.1374 0.1631 0.94 REMARK 3 4 3.62 - 3.29 0.93 16487 906 0.1629 0.1857 0.92 REMARK 3 5 3.29 - 3.05 0.93 16568 883 0.1837 0.2109 0.90 REMARK 3 6 3.05 - 2.87 0.94 16518 860 0.1793 0.2086 0.91 REMARK 3 7 2.87 - 2.73 0.94 16614 845 0.1880 0.2144 0.91 REMARK 3 8 2.73 - 2.61 0.94 16719 839 0.1904 0.2314 0.91 REMARK 3 9 2.61 - 2.51 0.92 16330 827 0.1983 0.2302 0.90 REMARK 3 10 2.51 - 2.42 0.91 16213 834 0.1975 0.2285 0.90 REMARK 3 11 2.42 - 2.35 0.95 16609 1002 0.1940 0.2298 0.90 REMARK 3 12 2.35 - 2.28 0.95 16777 956 0.2002 0.2385 0.90 REMARK 3 13 2.28 - 2.22 0.95 16840 860 0.2038 0.2425 0.89 REMARK 3 14 2.22 - 2.17 0.96 17010 942 0.2020 0.2355 0.89 REMARK 3 15 2.17 - 2.12 0.97 17059 880 0.2042 0.2325 0.89 REMARK 3 16 2.12 - 2.07 0.97 17221 906 0.2109 0.2458 0.88 REMARK 3 17 2.07 - 2.03 0.97 17215 906 0.2167 0.2377 0.86 REMARK 3 18 2.03 - 1.99 0.97 17288 852 0.2269 0.2581 0.87 REMARK 3 19 1.99 - 1.96 0.98 17264 909 0.2239 0.2558 0.86 REMARK 3 20 1.96 - 1.92 0.97 17222 875 0.2256 0.2642 0.85 REMARK 3 21 1.92 - 1.89 0.97 17217 857 0.2327 0.2573 0.83 REMARK 3 22 1.89 - 1.86 0.98 17346 979 0.2347 0.2767 0.82 REMARK 3 23 1.86 - 1.84 0.98 17292 941 0.2395 0.2591 0.82 REMARK 3 24 1.84 - 1.81 0.98 17267 893 0.2418 0.2657 0.81 REMARK 3 25 1.81 - 1.79 0.95 16887 859 0.2688 0.2934 0.77 REMARK 3 26 1.79 - 1.76 0.93 16540 850 0.2846 0.3100 0.74 REMARK 3 27 1.76 - 1.74 0.96 16937 908 0.2966 0.3255 0.72 REMARK 3 28 1.74 - 1.72 0.97 17121 881 0.3095 0.3275 0.70 REMARK 3 29 1.72 - 1.70 0.97 17057 934 0.3237 0.3415 0.68 REMARK 3 30 1.70 - 1.68 0.96 17088 881 0.3408 0.3717 0.66 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 GRID STEP FACTOR : 4.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.24 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.74 REMARK 3 REMARK 3 STRUCTURE FACTORS CALCULATION ALGORITHM : FFT REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.75 REMARK 3 REMARK 3 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. REMARK 3 BOND : 0.006 0.063 18548 Z= 0.330 REMARK 3 ANGLE : 0.854 15.131 25270 Z= 0.436 REMARK 3 CHIRALITY : 0.050 0.207 2961 REMARK 3 PLANARITY : 0.008 0.082 3280 REMARK 3 DIHEDRAL : 14.137 174.131 6734 REMARK 3 MIN NONBONDED DISTANCE : 1.885 REMARK 3 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 1.90 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.17 % REMARK 3 ALLOWED : 1.91 % REMARK 3 FAVORED : 97.93 % REMARK 3 ROTAMER OUTLIERS : 1.17 % REMARK 3 CBETA DEVIATIONS : 0.00 % REMARK 3 PEPTIDE PLANE: REMARK 3 CIS-PROLINE : 3.23 % REMARK 3 CIS-GENERAL : 0.00 % REMARK 3 TWISTED PROLINE : 0.00 % REMARK 3 TWISTED GENERAL : 0.00 % REMARK 3 REMARK 3 RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): REMARK 3 INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD REMARK 3 SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; REMARK 3 THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. REMARK 3 WHOLE: -0.51 (0.16), RESIDUES: 2418 REMARK 3 HELIX: -0.10 (0.13), RESIDUES: 1246 REMARK 3 SHEET: -0.72 (0.26), RESIDUES: 379 REMARK 3 LOOP : -0.18 (0.22), RESIDUES: 793 REMARK 3 REMARK 3 min max mean iso aniso REMARK 3 Overall: 14.31 89.25 29.87 2.50 20008 17938 REMARK 3 Protein: 14.31 89.25 29.51 2.50 17938 17938 REMARK 3 Water: 17.28 54.73 33.51 N/A 1781 0 REMARK 3 Other: 19.26 53.26 29.56 N/A 289 0 REMARK 3 Chain A: 16.68 89.25 29.50 N/A 9044 8987 REMARK 3 Chain B: 14.31 88.24 29.47 N/A 9012 8951 REMARK 3 Chain E: 25.39 33.97 29.46 N/A 44 0 REMARK 3 Chain F: 19.26 27.60 22.05 N/A 44 0 REMARK 3 Chain M: 34.40 39.36 36.19 N/A 3 0 REMARK 3 Chain P: 32.18 50.28 40.92 N/A 47 0 REMARK 3 Chain S: 17.28 54.73 33.51 N/A 1781 0 REMARK 3 Chain T: 21.64 53.26 37.38 N/A 30 0 REMARK 3 Chain X: 27.76 38.14 33.45 N/A 3 0 REMARK 3 Histogram: REMARK 3 Values Number of atoms REMARK 3 14.31 - 21.81 3292 REMARK 3 21.81 - 29.30 8566 REMARK 3 29.30 - 36.80 4360 REMARK 3 36.80 - 44.29 2144 REMARK 3 44.29 - 51.78 972 REMARK 3 51.78 - 59.28 379 REMARK 3 59.28 - 66.77 157 REMARK 3 66.77 - 74.27 99 REMARK 3 74.27 - 81.76 26 REMARK 3 81.76 - 89.25 13 REMARK 3 REMARK 3 REMARK 3 TLS DETAILS. REMARK 3 NUMBER OF TLS GROUPS: 2 REMARK 3 ORIGIN: CENTER OF MASS REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A and peptide REMARK 3 ORIGIN FOR THE GROUP (A): -26.0410 66.5091 93.2207 REMARK 3 T TENSOR REMARK 3 T11: 0.2116 T22: 0.1718 REMARK 3 T33: 0.1810 T12: 0.0121 REMARK 3 T13: 0.0145 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.5646 L22: 0.0929 REMARK 3 L33: 0.1416 L12: -0.0146 REMARK 3 L13: 0.1554 L23: -0.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.0694 S13: 0.0144 REMARK 3 S21: 0.0239 S22: 0.0226 S23: 0.0103 REMARK 3 S31: -0.0166 S32: -0.0142 S33: -0.0028 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain B and peptide REMARK 3 ORIGIN FOR THE GROUP (A): 5.5320 31.4735 91.7257 REMARK 3 T TENSOR REMARK 3 T11: 0.1668 T22: 0.1762 REMARK 3 T33: 0.1657 T12: 0.0032 REMARK 3 T13: 0.0030 T23: -0.0143 REMARK 3 L TENSOR REMARK 3 L11: 0.1947 L22: 0.2023 REMARK 3 L33: 0.3985 L12: 0.0090 REMARK 3 L13: 0.0872 L23: -0.0806 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: -0.0350 S13: -0.0133 REMARK 3 S21: 0.0406 S22: 0.0104 S23: -0.0032 REMARK 3 S31: 0.0372 S32: -0.1005 S33: -0.0276 REMARK 3 LINK N5 FDA A1400 C3 CBG A1401 LINK N5 FDA B1400 C3 ACBG B1401 LINK N5 FDA B1400 C3 BCBG B1401 LINK N5 FDA A1400 C3 CBG A1401 LINK N5 FDA B1400 C3 ACBG B1401 LINK N5 FDA B1400 C3 BCBG B1401 CRYST1 101.669 102.628 126.672 90.00 106.57 90.00 P 1 21 1 SCALE1 0.009836 0.000000 0.002927 0.00000 SCALE2 0.000000 0.009744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008236 0.00000 From: Patrick Loll Date: Sunday, October 15, 2023 at 4:55 PM To: Tanner, John J. , PHENIX user mailing list Subject: Re: [phenixbb] Renumbering while retaining refinement info Thanks Jack! Although I’m finding that Coot isn’t writing the refinement info in the output file either… (this is for deposition, so I need the refinement data). Maybe I need to try a newer version. On 15 Oct 2023, at 3:36 PM, Tanner, John J. mailto:[email protected]> wrote: External. Hi Pat, Coot has a tool to shift the residue numbers by a positive or negative increment. See Edit…Renumber Residues. Best Regards, Jack From: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Patrick Loll mailto:[email protected]> Date: Sunday, October 15, 2023 at 1:22 PM To: PHENIX user mailing list mailto:[email protected]> Subject: [phenixbb] Renumbering while retaining refinement info WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. Hello all, I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I’m working with a truncated construct (like a dope I didn’t do this at the outset). However, when I run PDB Tools, it does not write the refinement information into the output CIF. Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not so much in mmCIF). Cheers, Pat __________________________________ Patrick J. Loll, PhD (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St. Philadelphia, PA 19102-1192 USA (267) 359-2653 [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] Patrick Loll [email protected]mailto:[email protected]