Hi James, In addition to Thomas' answer... What is _wrong_ about the TER statement? Your chain is broken, indicated by the nonconsecutive numbers. That means you have two distinct molecules, and they are separated by a TER statement. Doesn't seem wrong. Yeah, they might be the same chain, but having a broken chain without considering them as separate molecules seems more wrong to me.
Cheers, Tsjerk On Tue, Mar 20, 2012 at 8:07 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Dear PyMol users! > > > After editing of my pdb files by means of PyMol I've noticed that some of my > structures contain of wrong TER enties in the body of the pdb files. In all > cases I save my processed pdb file by the PyMol context menu bar. > Below you can find xxample of processed file with the wrong TER enty: > > ATOM 1048 C GLN A 148 62.717 15.038 24.185 1.00159.20 > C > ATOM 1049 O GLN A 148 62.170 16.003 24.721 1.00160.85 > O > ATOM 1050 CB GLN A 148 60.966 14.990 22.391 1.00157.41 > C > ATOM 1051 CG GLN A 148 60.245 14.214 21.299 1.00164.79 > C > ATOM 1052 CD GLN A 148 61.187 13.683 20.234 1.00171.18 > C > ATOM 1053 OE1 GLN A 148 62.378 13.993 20.230 1.00175.57 > O > ATOM 1054 NE2 GLN A 148 60.654 12.880 19.321 1.00174.45 > N > ATOM 1055 N PRO A 149 63.997 14.705 24.415 1.00152.79 > N > ATOM 1056 CA PRO A 149 64.879 15.450 25.320 1.00137.09 > C > ATOM 1057 C PRO A 149 65.073 16.892 24.868 1.00130.60 > C > ATOM 1058 O PRO A 149 65.669 17.672 25.611 1.00127.66 > O > ATOM 1059 CB PRO A 149 66.204 14.689 25.221 1.00136.58 > C > ATOM 1060 CG PRO A 149 65.828 13.324 24.755 1.00144.26 > C > ATOM 1061 CD PRO A 149 64.668 13.530 23.836 1.00151.11 > C > TER 1062 PRO A 149 > ATOM 1063 N GLY A 158 65.079 6.711 35.576 1.00221.82 > N > ATOM 1064 CA GLY A 158 63.944 7.519 35.982 1.00219.41 > C > ATOM 1065 C GLY A 158 62.683 6.698 36.169 1.00218.58 > C > ATOM 1066 O GLY A 158 62.260 6.442 37.297 1.00218.85 > O > ATOM 1067 N CYS A 159 62.080 6.285 35.059 1.00216.88 > N > ATOM 1068 CA CYS A 159 60.855 5.496 35.100 1.00213.74 > C > ATOM 1069 C CYS A 159 61.030 4.163 34.379 1.00214.80 > C > ATOM 1070 O CYS A 159 60.118 3.336 34.354 1.00213.86 > O > ATOM 1071 CB CYS A 159 59.694 6.277 34.481 1.00211.79 > C > ATOM 1072 SG CYS A 159 59.342 7.859 35.283 1.00233.24 > S > ATOM 1073 N GLY A 160 62.206 3.961 33.794 1.00216.16 > N > ATOM 1074 CA GLY A 160 62.493 2.743 33.059 1.00217.18 > C > ATOM 1075 C GLY A 160 61.866 2.749 31.679 1.00215.69 > C > ATOM 1076 O GLY A 160 60.981 3.557 31.395 1.00214.72 > O > > In that example you can see the wrong string > TER 1062 PRO A 149 > > Some of my programs uncorrectly recognise such TER enties as the end of one > CHAIN and bigining of the another after TER. Could you tell me how I could > avoid of such TER after processing of my pdbs via PyMol ? > > Thanks for help > > > James > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
