[phenixbb] Renumbering while retaining refinement info
Tanner, John J.
TannerJJ at missouri.edu
Sun Oct 15 15:38:29 PDT 2023
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 <Bi,j> 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 <pjloll at gmail.com>
Date: Sunday, October 15, 2023 at 4:55 PM
To: Tanner, John J. <TannerJJ at missouri.edu>, PHENIX user mailing list <phenixbb at phenix-online.org>
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. <TannerJJ at missouri.edu<mailto:TannerJJ at missouri.edu>> 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: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>> on behalf of Patrick Loll <pjloll at gmail.com<mailto:pjloll at gmail.com>>
Date: Sunday, October 15, 2023 at 1:22 PM
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: [phenixbb] Renumbering while retaining refinement info
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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
pjl28 at drexel.edu<mailto:pjl28 at drexel.edu>
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