Oh dear - TLS transformations are a bag of worms! I usually start all over again if I want TLS .. SET all Bs to B_wilson Run 10 cycles of TLS with the groups listed in the PDB header.
That is boring but comparatively safe! Eleanor On 6 August 2017 at 15:36, Stefano Trapani <trap...@cbs.cnrs.fr> wrote: > Dear all > > I have found some issues in REFMAC5 output files (I am using version > 5.8.0158) > > 1) when I use the "pdbout shifts" instruction, the "TLS ORIGIN" values in > the TLSOUT file and the "REMARK 3" PDB records do not take into account the > applied origin shift > > 2) when I : > - do zero refinement cycles ("ncycles 0", just to calculate R-factors and > other statistics) > - set TLSIN = TLSOUT from a previous run > - do NOT use the "TLS ADDU" instruction > then the B factor values in the output PDB file will nevertheless contain > the contribution from the TLS tensors (not just the residuals B factors). > However, a "REMARK 3 U VALUES : RESIDUAL ONLY" card in the output > PDB file will be found. I have run some tests using coordinates and > structure factors from PDB entry 2pm1. You will find here below some > excerpts from the REFMAC5 log and output PDB files: > > #================================================================================ > ## RUN 0 : TLS + Biso refinement + TLSOUT addU > # refmac5 xyzin 2pm1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.0.pdb \ > # hklout refine.0.mtz \ > # tlsout refine.0.tls \ > # > > ./refine.0.log: Data line--- refi type rest reso 1.6 > ./refine.0.log: Data line--- refi bref iso > ./refine.0.log: Data line--- bfactor set 20 > ./refine.0.log: Data line--- refi tlsc 20 > ./refine.0.log: Data line--- ncycl 50 > ./refine.0.log: Data line--- tlsout addu > ./refine.0.log: Data line--- END > > ./refine.0.pdb:REMARK 3 U VALUES : WITH TLS ADDED > ./refine.0.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 > 24.39 N > ./refine.0.pdb:ANISOU 1 N ALA A 1 3480 3008 2779 -684 > -267 -1026 N > ./refine.0.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 > 21.59 C > ./refine.0.pdb:ANISOU 2 CA ALA A 1 2947 2814 2439 -575 > -360 -773 C > ./refine.0.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 > 22.81 C > ./refine.0.pdb:ANISOU 3 CB ALA A 1 3184 3199 2282 -488 > -498 -713 C > ./refine.0.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 > 18.64 C > ./refine.0.pdb:ANISOU 4 C ALA A 1 2551 2314 2214 -438 > -179 -575 C > ./refine.0.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 > 19.23 O > ./refine.0.pdb:ANISOU 5 O ALA A 1 2730 2280 2294 -344 > -6 -574 O > ================================================================================ > ## RUN 1 : TLS+Biso refinement; no TLSOUT addU > # refmac5 xyzin 2pm1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.1.pdb \ > # hklout refine.1.mtz \ > # tlsout refine.1.tls \ > # > > ./refine.1.log: Data line--- refi type rest reso 1.6 > ./refine.1.log: Data line--- refi bref iso > ./refine.1.log: Data line--- bfactor set 20 > ./refine.1.log: Data line--- refi tlsc 20 > ./refine.1.log: Data line--- ncycl 50 > ./refine.1.log: Data line--- END > > ./refine.1.pdb:REMARK 3 U VALUES : RESIDUAL ONLY > ./refine.1.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 > 11.25 N > ./refine.1.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 > 10.71 C > ./refine.1.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 > 11.12 C > ./refine.1.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 > 10.38 C > ./refine.1.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 > 11.15 O > ================================================================================ > ## RUN 2a : run 0 TLScycles + 0 REFI cycles starting from run 1 output > # refmac5 xyzin refine.1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.2a.pdb \ > # hklout refine.2a.mtz \ > # tlsin refine.1.tls \ > # tlsout refine.2a.tls \ > # > > ./refine.2a.log: Data line--- refi type rest reso 1.6 > ./refine.2a.log: Data line--- refi bref iso > ./refine.2a.log: Data line--- refi tlsc 0 > ./refine.2a.log: Data line--- ncycl 0 > ./refine.2a.log: Data line--- END > ./refine.2a.log: Data line--- REFMAC_5.8.0158 > ./refine.2a.log: Data line--- TLS From REFMAC > ./refine.2a.log: Data line--- RANGE 'A 1.' 'A 83.' ALL > ./refine.2a.log: Data line--- ORIGIN 14.408 -11.294 0.204 > ./refine.2a.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 > -0.0132 0.0145 > ./refine.2a.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 > -1.0778 0.8265 > ./refine.2a.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 > 0.2451 0.0292 0.2475 -0.3305 > > ./refine.2a.pdb:REMARK 3 U VALUES : RESIDUAL ONLY > ./refine.2a.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 > 24.39 N > ./refine.2a.pdb:ANISOU 1 N ALA A 1 3480 3008 2779 -684 > -267 -1026 N > ./refine.2a.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 > 21.59 C > ./refine.2a.pdb:ANISOU 2 CA ALA A 1 2948 2814 2439 -575 > -360 -773 C > ./refine.2a.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 > 22.81 C > ./refine.2a.pdb:ANISOU 3 CB ALA A 1 3185 3198 2282 -488 > -498 -713 C > ./refine.2a.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 > 18.64 C > ./refine.2a.pdb:ANISOU 4 C ALA A 1 2552 2314 2214 -438 > -179 -576 C > ./refine.2a.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 > 19.23 O > ./refine.2a.pdb:ANISOU 5 O ALA A 1 2731 2281 2295 -344 > -7 -574 O > ================================================================================ > ## RUN 2b : run 1 TLS cycle + 1 REFI cycle starting from run 1 output > # refmac5 xyzin refine.1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.2b.pdb \ > # hklout refine.2b.mtz \ > # tlsin refine.1.tls \ > # tlsout refine.2b.tls \ > # > > ./refine.2b.log: Data line--- refi type rest reso 1.6 > ./refine.2b.log: Data line--- refi bref iso > ./refine.2b.log: Data line--- refi tlsc 1 > ./refine.2b.log: Data line--- ncycl 1 > ./refine.2b.log: Data line--- END > ./refine.2b.log: Data line--- REFMAC_5.8.0158 > ./refine.2b.log: Data line--- TLS From REFMAC > ./refine.2b.log: Data line--- RANGE 'A 1.' 'A 83.' ALL > ./refine.2b.log: Data line--- ORIGIN 14.408 -11.294 0.204 > ./refine.2b.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 > -0.0132 0.0145 > ./refine.2b.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 > -1.0778 0.8265 > ./refine.2b.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 > 0.2451 0.0292 0.2475 -0.3305 > > ./refine.2b.pdb:REMARK 3 U VALUES : RESIDUAL ONLY > ./refine.2b.pdb:ATOM 1 N ALA A 1 19.624 -3.183 8.094 1.00 > 11.31 N > ./refine.2b.pdb:ATOM 2 CA ALA A 1 19.857 -4.525 7.537 1.00 > 10.72 C > ./refine.2b.pdb:ATOM 3 CB ALA A 1 19.749 -5.555 8.682 1.00 > 11.14 C > ./refine.2b.pdb:ATOM 4 C ALA A 1 18.904 -4.806 6.397 1.00 > 10.38 C > ./refine.2b.pdb:ATOM 5 O ALA A 1 17.697 -4.379 6.389 1.00 > 11.21 O > ================================================================================ > ## RUN 2c : run 1 TLS cycle + 0 REFI cycle starting from run 1 output > # refmac5 xyzin refine.1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.2c.pdb \ > # hklout refine.2c.mtz \ > # tlsin refine.1.tls \ > # tlsout refine.2c.tls \ > # > > ./refine.2c.log: Data line--- refi type rest reso 1.6 > ./refine.2c.log: Data line--- refi bref iso > ./refine.2c.log: Data line--- refi tlsc 1 > ./refine.2c.log: Data line--- ncycl 0 > ./refine.2c.log: Data line--- END > ./refine.2c.log: Data line--- REFMAC_5.8.0158 > ./refine.2c.log: Data line--- TLS From REFMAC > ./refine.2c.log: Data line--- RANGE 'A 1.' 'A 83.' ALL > ./refine.2c.log: Data line--- ORIGIN 14.408 -11.294 0.204 > ./refine.2c.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 > -0.0132 0.0145 > ./refine.2c.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 > -1.0778 0.8265 > ./refine.2c.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 > 0.2451 0.0292 0.2475 -0.3305 > > ./refine.2c.pdb:REMARK 3 U VALUES : RESIDUAL ONLY > ./refine.2c.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 > 24.22 N > ./refine.2c.pdb:ANISOU 1 N ALA A 1 3456 2974 2771 -686 > -241 -1002 N > ./refine.2c.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 > 21.45 C > ./refine.2c.pdb:ANISOU 2 CA ALA A 1 2928 2783 2437 -578 > -335 -755 C > ./refine.2c.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 > 22.64 C > ./refine.2c.pdb:ANISOU 3 CB ALA A 1 3156 3160 2286 -496 > -469 -696 C > ./refine.2c.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 > 18.57 C > ./refine.2c.pdb:ANISOU 4 C ALA A 1 2540 2292 2220 -439 > -161 -563 C > ./refine.2c.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 > 19.18 O > ./refine.2c.pdb:ANISOU 5 O ALA A 1 2718 2262 2304 -345 > 8 -562 O > ================================================================================ > ## RUN 2d : run 0 TLS cycle + 1 REFI cycle starting from run 1 output > # refmac5 xyzin refine.1.pdb \ > # hklin 2pm1_unique.mtz \ > # xyzout refine.2d.pdb \ > # hklout refine.2d.mtz \ > # tlsin refine.1.tls \ > # tlsout refine.2d.tls \ > # > > ./refine.2d.log: Data line--- refi type rest reso 1.6 > ./refine.2d.log: Data line--- refi bref iso > ./refine.2d.log: Data line--- refi tlsc 0 > ./refine.2d.log: Data line--- ncycl 1 > ./refine.2d.log: Data line--- END > ./refine.2d.log: Data line--- REFMAC_5.8.0158 > ./refine.2d.log: Data line--- TLS From REFMAC > ./refine.2d.log: Data line--- RANGE 'A 1.' 'A 83.' ALL > ./refine.2d.log: Data line--- ORIGIN 14.408 -11.294 0.204 > ./refine.2d.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 > -0.0132 0.0145 > ./refine.2d.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 > -1.0778 0.8265 > ./refine.2d.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 > 0.2451 0.0292 0.2475 -0.3305 > > ./refine.2d.pdb:REMARK 3 U VALUES : RESIDUAL ONLY > ./refine.2d.pdb:ATOM 1 N ALA A 1 19.621 -3.183 8.093 1.00 > 11.24 N > ./refine.2d.pdb:ATOM 2 CA ALA A 1 19.857 -4.524 7.537 1.00 > 10.69 C > ./refine.2d.pdb:ATOM 3 CB ALA A 1 19.748 -5.555 8.682 1.00 > 11.10 C > ./refine.2d.pdb:ATOM 4 C ALA A 1 18.905 -4.806 6.397 1.00 > 10.36 C > ./refine.2d.pdb:ATOM 5 O ALA A 1 17.698 -4.380 6.390 1.00 > 11.19 O > > > > -- > Stefano Trapani > > Maître de > Conférenceshttp://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani > ------------------------------------- > Centre de Biochimie Structurale (CBS) > 29 rue de Navacelles > 34090 MONTPELLIER Cedex, France > > Tel : +33 (0)4 67 41 77 29 <+33%204%2067%2041%2077%2029> > Fax : +33 (0)4 67 41 79 13 <+33%204%2067%2041%2079%2013> > ------------------------------------- > Université de Montpellier > CNRS UMR 5048 > INSERM UMR 1054 > ------------------------------------- > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is > believed to be clean. >