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Re: [ccp4bb] PHASER packing function with DNA |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: PHASER packing function with DNA From: LEDU Marie-Helene 161111 Marie-Helene {- dot -} LEDU {- at -} CEA {- dot -} FR Date: 2009-08-06 Hi, Thanks a lot for the replies. It seems that Randy¹s solution works fine. Marie-Ln Le 6/08/09 13:54, « Randy Read » > Hi, > > That's actually the last question answered on our FAQ page! > > http://www-structmed.cimr.cam.ac.uk/phaser/faq.html > > Basically, you'll want to change lines like this: > ATOM 1 P Gd C 1 23.560 11.045 11.025 1.00 53.18 P > to lines like this: > ATOM 1 P G C 1 23.560 11.045 11.025 1.00 53.18 P > because Phaser 2.1.4 expects the residue name in one-letter code in column 20. > > We didn't notice, before releasing version 2.1.4, that one effect of the PDB > remediation was to change the nomenclature for nucleic acid residues, so the > packing check won't work using files recently obtained from the PDB (where > deoxy-G is represented as DG in columns 19-20). This is fixed for version > 2.2.x (available as part of Phenix nightly builds, and hopefully from an > upcoming CCP4 release); in the meantime, you'll have to edit recent PDB files > before running Phaser. > > Best wishes, > > Randy Read > > On 6 Aug 2009, at 11:25, LEDU Marie-Helene 161111 wrote: > >> Dear CCP4BBer, >> >> I'm using Phaser 2.1.4 to solve a structure containing both protein and DNA. >> The packing function works find with the protein, but does not recognize the >> trace of the DNA. Does anyone know precisely what should be the pdb format ? >> Here is the format that I'am using : >> ATOM 1 P Gd C 1 23.560 11.045 11.025 1.00 53.18 >> P >> ATOM 2 OP1 Gd C 1 24.884 10.499 11.417 1.00 54.98 >> O >> ATOM 3 OP2 Gd C 1 22.319 10.778 11.791 1.00 44.44 >> O >> ATOM 4 O5' Gd C 1 23.716 12.601 10.891 1.00 47.89 >> O >> ATOM 5 C5' Gd C 1 24.689 13.001 9.945 1.00 42.99 >> C >> ATOM 6 C4' Gd C 1 24.395 14.391 9.437 1.00 39.27 >> C >> ATOM 7 O4' Gd C 1 23.172 14.464 8.683 1.00 35.25 >> O >> ATOM 8 C3' Gd C 1 24.264 15.347 10.617 1.00 36.72 >> C >> ATOM 9 O3' Gd C 1 25.063 16.487 10.335 1.00 34.52 >> O >> ATOM 10 C2' Gd C 1 22.807 15.691 10.507 1.00 34.06 >> C >> ATOM 11 C1' Gd C 1 22.474 15.641 9.080 1.00 27.89 >> C >> ATOM 12 N9 Gd C 1 21.218 15.303 8.921 1.00 20.00 >> N >> ATOM 13 C8 Gd C 1 20.436 14.344 9.523 1.00 20.00 >> C >> ATOM 14 N7 Gd C 1 19.207 14.292 9.056 1.00 20.00 >> N >> ATOM 15 C5 Gd C 1 19.159 15.275 8.076 1.00 20.00 >> C >> ATOM 16 C4 Gd C 1 20.381 15.912 7.978 1.00 20.00 >> C >> ATOM 17 N1 Gd C 1 18.457 16.733 6.390 1.00 20.00 >> N >> ATOM 18 C2 Gd C 1 19.700 17.306 6.353 1.00 20.00 >> C >> ATOM 19 N3 Gd C 1 20.705 16.934 7.129 1.00 20.00 >> N >> ATOM 20 C6 Gd C 1 18.087 15.691 7.242 1.00 20.00 >> C >> ATOM 21 O6 Gd C 1 16.928 15.244 7.199 1.00 20.00 >> O >> ATOM 22 N2 Gd C 1 19.883 18.288 5.476 1.00 20.00 >> N >> >> Thanks, >> >> Marie-Ln >> >> Laboratoire de Biologie Structurale et Radiobiologie >> CEA/DSV/IBiTec-S/SB2SM >> bat144, pièce 25 >> 91191 Gif-Sur-Yvette >> Tel : 33 (0)1 69 08 71 35 >> E-mail : marie-helene.ledu@cea.fr >> -- >> >> >> >> > > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: rjr27@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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