[modeller_usage] Metal ions

-- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 MODELLER 8v2, Feb 28, 2006 05:48pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2006 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux allroy.otago.ac.nz 2.6.9-5.ELsmp x86_64 Date and time of compilation : 02/28/2006 18:38:42 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/07/07 09:55:15.134 rdabrk__290E> Number of residues in the alignment and pdb files are different: 66 65 For alignment entry: 1 2fk4 x (mismatch at alignment position 66) Alignment FHNIRGRWTGRCMSCSRSSRz PDB FHNIRGRWTGRCMSCSRSSR Match ******************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. check_a_337E> Structure not read in (please consult the log file for more details): 1 2fk4 top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2331663 2277.015 2.224 Starting time : 2006/07/07 09:55:15.134 Closing time : 2006/07/07 09:55:16.008 Total CPU time [seconds] : 0.87 INCLUDE SET ALNFILE = 'hpv_16_e6_Nterm_2fk4.ali' SET KNOWNS = '2fk4' SET SEQUENCE = 'hpv_16_Nterm_e6' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' SET HETATM_IO = on >P1;2fk4 structureX:2fk4: 3 :A: 68 ::::: SYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSR/z* >P1;hpv_16_Nterm_e6 sequence:hpv_16_Nterm_e6: : : : ::: 0.00: 0.00 PRKLP--QLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYS/z*