- modeller_usage - salilab.org

can't find Log file
by Dong Chen 08 Apr '03

08 Apr '03

Hi All, After sending e-mail yesterday, I received several e-mails and all told me I should see the .log file in the same directory. But I am sure there is no .log file in the directory. I am using MODELLER 6v2 for Windows and my operation system is Window 2000. I run "mod model-default" in windows command prompt "C:\mod6v2\examples\tutorial-model>". Following is the model-default.top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling After running "mod model-default", I only got six files: "1fdx.V99990001, 1fdx.D00000001, 1fdx.B99990001, 1fdx.sch, 1fdx.rsr and 1fdx.ini. I can open the 1fdx.B99990001 by a viewer. Thanks for all your help, Dong

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Questions about using Modeller
by Dong Chen 07 Apr '03

07 Apr '03

Hi, I am just starting using Modeller and have two questions about it. 1. After I run "mod model-default" in the tutorial, I can't not find the model-default.log file. Where to find this log file? 2. I have seen the some output data in 1fdx.B99990001. Is it possible for me to convert the data in 1fdx.B99990001 to a 3D structure? My OS is Windows 2000 and using MODELLER 6v2. Thank you for any help, Dong

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Running Modeller6v2 Windows
by Anurag Sethi 07 Apr '03

07 Apr '03

Hi, I am new to Modeller. I am having problems running the modeller windows version on XP. I am trying to run the following top file using the command: mod model-default.top INCLUDE READ_ALIGNMENT DIRECTORY = 'C:\mod6v2\alignments', FILE = '1L9H_O2D2.ali', ALIGNMENT_FORMAT = 'PIR' SET KNOWNS = '1l9h' SET SEQUENCE = 'O2D2' SET ATOM_FILES_DIRECTORY = 'C:\mod6v2\pdb', ATOM_FILES = '1l9h.atm' SET OUTPUT_CONTROL = 1 1 1 1 1 SET STARTING_MODEL = 1 SET ENDING_MODEL = 3 CALL ROUTINE = 'model' The alignment file is itself >1l9h >structure:1l9h:1 :A:349:A:Bacterorhodopsin:Archae Bacteria:1.5:-1 ---MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKK LRT------PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVF---------GPTGCNLEGFFATLGGE IALWSLVVLAIERYVVVCKPMSNFRFG----------ENHAIMGVAFTWVMALACAAPPLVGWSRYIPEG MQCSCGIDYYTPHEETN--------NESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA-----ATT- -QKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQ FRNCMVTTLCCGKNPLGD---STTVSKTETSQVAPA >O2D2 sequence:O2D2:1: :308: :1:1 MRQINQTQVTEFLL-----LGLSDGPHTEQ------LLFIVLLGVY--LVTVLG---NLLLISL---VHV DSQLHTPMYFFLCNLSLADLCFSTNIVPQALV-------HLLSRKKVIAFTLCAARLLFFLIFGCTQCAL LAVMSY-----------DRYVAICNPLRYPDIMTWKVCVQLATGSWTSGILVSVVDTTFT-LRLPYRGSN SIAHFFCEAPALLILASTDTHASEMAIFLTGVVILLIPVFLILVSYGR---IIVTVVKMKSTVGSLKAFS TCGSHLMVVILF------YGSAIITYMTPK-----SSKQQEKSV--------------SVFYAIVTPMLN PLIYSLR--NKDVKAAL--------RKVATRNF-P- The log file I got is: C:\mod6v2\bin>set MODINSTALL6v2=c:\mod6v2 C:\mod6v2\bin>set KEY_MODELLER6v2=$The key i got$ C:\mod6v2\bin>set LIBS_LIB6v2=c:\mod6v2\modlib\libs.lib C:\mod6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf C:\mod6v2\bin>set PATH=c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Adaptec Shared\System;c:\matlab6p1\bin\win32;C:\Program Files\SSH Communications Security\SSH Secure Shell;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin;c:\mod6v2\bin C:\mod6v2\bin>c:\mod6v2\bin\modeller6v2 model-default.top MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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, Windows_NT SETHI x86 Family 15 Model 2 Stepping 7, GenuineIn Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/07 06:33:47.390 TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 3 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2560929 2500.907 2.442 openf5__224_> Open 11 OLD SEQUENTIAL \mod6v2\alignments/ openf5__228E> Error openning file: \mod6v2\alignments/ recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2560929 2500.907 2.442 Starting time : 2003/04/07 06:33:47.390 Closing time : 2003/04/07 06:33:49.687 Total CPU time [seconds] : 1.92 I dont know whether this is an error of mine or is it that I havent installed it properly or that my top file is wrong. Could someone please help me out? Thank you in advance, Anurag Sethi

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residue-undefined
by Modeller Care 01 Apr '03

01 Apr '03

forwarded by the list owner ------------------------------------------------------------- Dear MODELLER users, I am facing this problem while running MODELLER. I am trying to model a protein and I want to model HEME cofactor also in the model using the template having HEME. I have indicated in the alignment file the heme symbol "h". But I am getting an error message saying residue type not defined. It dosen't say as which residue is not defined also. I could not solve the problem even after long trying. Probably it may be because of a basic mistake in the input. I would be grateful to you if any of you solve this problem. I attach the ali file top file and also the log file returned by MODELLER. Thanks. sridhar ------ End of Forwarded Message

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heteroatoms_zinc
by Alys.Peisley＠csiro.au 01 Apr '03

01 Apr '03

Hi all, i'm trying to get modeller to include a zinc atom in my model. I have mastered the art ofgetting teh zinc read into the program, however the model it produces has the zinc miles away and the coordinating residues stubbornly unligated. How does one go about instructing modeller to coordinate the zinc atom. I have a histine and a asp coordinating it. i have attached my alignment and inputfiles regards Alys [pei015@freedom model_zinc]$ more xmera_1.ali >P1;1BP3 structureX:1BP3: 214 :A: 413 :A:undefined:undefined:-1.00:-1.00 ---------------SPNKE-TF/-------------------- -------HREG--ETLM/---------------------------HFGKQYTS--MWRT/------------------------- -----------YVDVTY/-------------------------------LIDLKTGWFT/--------------- ------------FAG-Q/--------------------------KP--DHGY/----------------------/z* >P1;1N26 structureX:1N26: 92 :A: 299 :A:undefined:undefined:-1.00:-1.00 DVP--PEEPQL-SCF--------RKSPLSNVVCEWGPRSTPSLT TKAVLLV----------RKFQNSPAEDFQEPCQY--SQESQKFSC--------------QL---AVPEGDSSFYIVSMCVASSVG SKFS----KTQTFQGCGILQPDPPANITVTAVAR--NPRWLSVTWQDPH----------SWNSS-F-YRLRFELR YRAERSKTFTTW------MVKDLQHHCVIHDAWSGLRHVVQLRA--------QEEFGQGEWSEWSPEAMGTPWTES/-* >P1;1xmera sequence:1xmera: : : : :undefined:undefined:-1.00:-1.00 DVP--PEEPQL-SCFSPNKE-TF--------VCEWGPRSTPSLT TKAVLLVHREG--ETLM----------FQEPCQY--SQESQKFSCHFGKQYTS--MWRT--------------YIVSMCVASSVG SKFS----DELYVDVTYILQPDPPANITVTAVAR--NPRWLSVTWQDPHLIDLKTGWFT----------LRFELR YRAERSKTFTTWFAG-Q------QHHCVIHDAWSGLRHVVQLRAKP--DHGY--------WSEWSPEAMGTPWTES/z* the top file is [pei015@freedom model_zinc]$ more build_model.top INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'xmera_1.ali' SET KNOWNS = '1BP3' '1N26' SET SEQUENCE = '1xmera' SET HETATM_IO = on CALL ROUTINE = 'model'

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modeller question
by Modeller Care 31 Mar '03

31 Mar '03

Darren, it looks like you executed modeller without giving it a .top file. Best, ursula Forwarded by the list owner: ------ Forwarded Message From: owner-modeller_usage(a)salilab.org Date: Sun, 30 Mar 2003 18:42:39 -0800 To: modeller_usage-approval(a)salilab.org Subject: BOUNCE modeller_usage(a)salilab.org: Non-member submission from [Darren Thompson <thompson(a)chemistry.ucsc.edu>] whenever I try and run the executable mod6v2_mac10v2-absoft i get MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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, Darwin Darren-Thompsons-Computer.local. 6.4 Power Mac intosh Date and time of compilation : 10/06/2002 20:50:17 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/30 18:20:11.379 fullfn__230E> File not found: mod Directories: :${MODINSTALL6v2}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2003/03/30 18:20:11.379 Closing time : 2003/03/30 18:20:14.284 Total CPU time [seconds] : 2.17 STOP and %mod6v2 usage: mod script[.top] % where is this mod script any help would be appreciated Darren A. Thompson Researcher UCSC 1156 High St. Santa Cruz, CA 95064 voice: 831-459-3390 fax: 831-459-2935 http://people.ucsc.edu/~ministry ------ End of Forwarded Message

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modeller from python
by Ursula Pieper 31 Mar '03

31 Mar '03

Abhinav, We don't have experience with python, but my guess is that some environment variables are not set properly. Best regards, Ursula --- Ursula Pieper temporary modeller caretaker Message forwarded by the listowner: ------------------------------------------------------------------------ Dear Andrej, I am having a small problem regarding running modeller from a python script. Can you let me know some solution. The program terminates after generating .ini file. Do I need to run modeller from command line only. I use the system commands in python script(os.system('mod6v2 xyz')) Hoping to hear from you soon. Best Regards, Abhinav.

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MAXATM
by Matteo Masetti 31 Mar '03

31 Mar '03

Dear all, I am using Modeller6v2 running on a PC Linux machine (OS RedHat 8.0; kernel version 2.4.28), and i'm trying to build the model of a symmetric tetrameric protein. I met the following problem: after the building of 2 models out of ten, modeller stops with the following error message: define__223E> Array too small. Increase MAXATM current maximum, current need: 3228 3229 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 We don't have the source files: please, may you help me?

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Re: Re: Modeller6v2 installation problem
by Kong Lesheng 23 Mar '03

23 Mar '03

Dear Dr. Bozidar Yerkovich, I have added RTF of HYP into Modeller6v2 library. With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 ---------------------------------

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Re: Re: Modeller6v2 installation problem
by Kong Lesheng 23 Mar '03

23 Mar '03

Dear Dr. Bozidar Yerkovich, I have added RTF of HYP into Modeller6v2 library. With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 ---------------------------------

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