July 2006 - modeller_usage

Model assessment - GA341
by Cassiano 08 Jul '06

08 Jul '06

Hi all, I have some questions about the model.asses_ga341. In the manual on-line is described that it uses the "percentage sequence identity between the template and the model as a parameter". But, in the cited work (Melo et al, 2002) i don't see this relation with sequence identity. My questions: - How Modeller treat the sequence identity in the context of the cited work? - If the identity between my target and templates is very low, how the quality of the model is affected? (and what you recommend to use to assess the quality) Thanks, Cassiano Carromeu.

2 1

Metal ions
by Joel Tyndall 06 Jul '06

06 Jul '06

Hi message board, I have been trying to include a zinc atom in my model based on the same ion in the template but I just can't crack it. I have attached all relevant files and log file. I am using mod8v2. Advice is much appreciated Cheers Joel -- 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*

2 1

I have problem my protien has some area seems to be extra
by Zartasha Mustansar 03 Jul '06

03 Jul '06

My template is single ... The generated output models (i created 10 moedls with modeller) the model with best energy has some area leaning out of the structure which seems to be not included in the protien ....(When Viewed with Swiss pdb Viewer) How could i made it fit to the alignment with template. i m attaching that output file with it. its a sequence of a Baffalo family (Nili ravi); Thanx! -- Zartasha Mustansar. Sky May be the limit for others ! But it is just The Beginning For Us..! ( ~ Islamians..) -----------------------------(The competitive Bio-Informaticians ! )--------------------------

2 1

modeller
by Patrycja Barbara Lewkowicz 01 Jul '06

01 Jul '06

Hello ! I was trying to make a model in modeller and there's one problem that occured: return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in: 1 Can you help me? It's a new program for me and I acctually have no idea what it wrong. thank you for help Patrycja

2 1