Hi All I think that is the reason. In version of refmac (with new dictio uses new pdb v3 hydrogen naming and there are a lot of differences.
regards Garib On 28 Oct 2011, at 10:00, LEGRAND Pierre wrote: > Hi Kenneth, > > I am experiencing exactly the same problem, in similar conditions: refinement > with H at 0.84 A resolution. >> From a bunch of tests made yesterday, I have found that it is linked to >> incompatibilities between cif dictionaries definitions and H names in the >> input PDB. > For me, one simple solution to that problem, was to remove all H atoms from > my input pdb and let refmac rebuild them (MAKE HYDR ALL). > I hope the trick will work for you. > > By the way, I am facing an other problem: Clashes in inter residues H-bonds > between H and acceptor atoms. What is the correct way to define these. The > HYDBND pdb definition doesn't seems to work. Do I need to use LINK > definitions ? Is there a way to do that automatically ? > > Cheers, > Pierre > > ________________________________ > De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Robbie Joosten > [robbie_joos...@hotmail.com] > Date d'envoi : vendredi 28 octobre 2011 09:42 > À : CCP4BB@JISCMAIL.AC.UK > Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 > > Hi Kenneth, > > This looks like an off-by-one bug in the restraint generation. Typical > sources are weird LINKs, wrong atom names and bad luck. I suggest you make > sure you have the very latest Refmac and dictionary and try setting up a new > refinement instead of recycling an old job. If that doesn't work, we may need > a closer look at your input model. > > Cheers, > Robbie > >> Date: Thu, 27 Oct 2011 20:48:49 -0500 >> From: satys...@wisc.edu >> Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 >> To: CCP4BB@JISCMAIL.AC.UK >> >> Has anyone had problems with Refmac 5.6? I tried refining our stucture at >> 1.24 A, >> aniso with H in riding position and it just exploded! I get error in >> distances such as >> >> Standard External All >> Bonds: 3270 0 3270 >> Angles: 4923 0 4923 >> Chirals: 214 0 214 >> Planes: 368 0 368 >> Torsions: 957 0 957 >> --------------------------------------- >> >> Number of reflections in file 90428 >> Number of reflections read 90428 >> >> >> CGMAT cycle number = 1 >> >> **** Bond distance outliers >> **** >> >> Bond distance deviations from the ideal >10.000Sigma will be monitored >> >> A 5 PRO C A - A 5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015 >> sig.= 0.014 >> A 5 PRO C B - A 5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668 >> sig.= 0.014 >> A 5 PRO HB1 A - A 5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834 >> sig.= 0.021 >> A 5 PRO HB1 A - A 6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547 >> sig.= 0.020 >> A 5 PRO HB1 B - A 5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789 >> sig.= 0.021 >> A 5 PRO HB1 B - A 6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669 >> sig.= 0.020 >> A 5 PRO HG1 A - A 5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287 >> sig.= 0.020 >> A 5 PRO HG1 A - A 6 LEU N A mod.= 4.860 id.= 1.530 dev= -3.330 >> sig.= 0.020 >> A 5 PRO HG1 A - A 6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604 >> sig.= 0.021 >> A 5 PRO HG1 B - A 5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256 >> sig.= 0.020 >> A 5 PRO HG1 B - A 6 LEU N B mod.= 4.922 id.= 1.530 dev= -3.392 >> sig.= 0.020 >> A 5 PRO HG1 B - A 6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139 >> sig.= 0.021 >> A 6 LEU N A - A 6 LEU CA A mod.= 1.467 id.= 0.970 dev= -0.497 >> sig.= 0.020 >> A 6 LEU N A - A 6 LEU HA A mod.= 2.005 id.= 0.970 dev= -1.035 >> sig.= 0.020 >> A 6 LEU N A - A 6 LEU CB A mod.= 2.497 id.= 1.530 dev= -0.967 >> sig.= 0.020 >> A 6 LEU N B - A 6 LEU CA B mod.= 1.469 id.= 0.970 dev= -0.499 >> sig.= 0.020 >> A 6 LEU N B - A 6 LEU HA B mod.= 2.032 id.= 0.970 dev= -1.062 >> sig.= 0.020 >> A 6 LEU N B - A 6 LEU CB B mod.= 2.446 id.= 1.530 dev= -0.916 >> sig.= 0.020 >> A 6 LEU CB A - A 6 LEU HB2 A mod.= 0.969 id.= 1.521 dev= 0.552 >> sig.= 0.020 >> A >> >> Rfree goes form 17 to 28 and R from 15 to 25. >> Coot map looks like a bunch of busted insect parts. >> >> >> I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is good. >> I am forced to use the >> old ccp4 and refmac to publish. Rf 17 R 15. >> thanks >> >> -- >> Kenneth A. Satyshur, M.S.,Ph.D. >> Associate Scientist >> University of Wisconsin >> Madison, Wisconsin 53706 >> 608-215-5207 Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
