- modeller_usage - salilab.org

modeling question
by Douglas Kojetin 12 May '03

12 May '03

please see the message, originally directed towards dr. sali, below. if anyone has any comments, please send them! many thanks, doug kojetin Begin forwarded message: > Dr. Sali: > > I am a graduate student in the Department of Molecular and Structural > Biochemistry at North Carolina State University. I have a question > more about modeling process itself rather than the program MODELLER. > > I have used your program, MODELLER, to create models of a subfamily of > proteins our lab and collaborators are interested in (total ~ 30). > There are approximately 10 solved structures to the domain of > interest. One of these solved structures (structure A) is in the same > subfamily within the same species of proteins we are modeling (model > A), whereas the other 29 proteins are of unknown solved structure. My > question concerning the use of templates in the modeling process. > > ############## > my main question > ############## > > (if this is confusing, please let me know and i will rephrase) ... > > Would using a solved structure (structure A) to model a protein of > exact sequence (model A) which will be used in a comparison of 29 > other structures with no known structures (and lower 'homology' > compared to that of structure A to model A -- which is 100%) bias > model A? Overall, we are interested in comparing all 30 structures. > This comes mostly from outside comments that our modeled protein does > not look 'exactly' like the solved structure. As one would like it to > look as close as possible to the solved structure, it is a model after > all, and perhaps we just need to be more descriptive in explaining our > results, especially pertaining to this specific model. > > ##################### > how i modeled the proteins > ##################### > > I performed a 'modeling parameter assay' to find the number of > templates to use to model a protein (model B), ranging from 1 to ~8 > templates. In addition, I 'assayed' the amount of refinement to use. > > Overall, I had an assay 'shaped' like a matrix with, for example, > refinement across the top and # of templates going down. I produced 50 > models for each and ran a variety of analyses on the models (including > Ca RMSD to the most homologous protein, ERRAT, PROCHECK, etc) and > computed the average 'value' output from the respective analyses. > > All in all, using four (4) templates and a refinement value of 1 > produced the 'stereochemically best' models. > > I applied the same rationale to another protein of interest (model C), > and the same trends were extrapolated. > > question > --> is this rationale 'acceptable'? or how would you do something > similar? > > Many thanks for your input, and I'm sorry for the long-winded email. > > Douglas Kojetin

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malign3D
by Modeller Care 07 May '03

07 May '03

Message forwarded by list-owner (log file delete because of encoding error) --------------------------------------------------- Dear sir, I'll be very much grateful to you if you can help me in one of my modeller job submission. I am trying to superimpose some structures simultaneously using malign3D. My top script file and alignment file are as follows. I had attached the log file also. There structures were of ~410 residues and with heme and a bound ligand. I always failed to get the structural alignment, the reason I could not figure out. Please help me in running this program, also tell me what are the general steps to follow for doing structural alignments and where are the chances for potential errors. ###########################TOP SCRIPT################## SET OUTPUT_CONTROL = 1 1 1 1 2 SET STOP_ON_ERROR = 1 SET MAXRES = 2000 READ_ALIGNMENT FILE = 'str.ali' SEQUENCE_TO_ALI SET ALIGN_CODES = '1dz8' '2cpp' SET ATOM_FILES = ALIGN_CODES SET ATOM_FILES_DIRECTORY = './' MALIGN3D SET ADD_SEQUENCE = on SET CURRENT_DIRECTORY = on SET OUTPUT = 'LONG' SET GAP_PENALTIES_3D = 0.0 1.75 SET FIT_ATOMS = 'CA' SET WRITE_FIT = on SET WRITE_WHOLE_PDB = on WRITE_ALIGNMENT FILE = 'str_STR.pir' SET ALIGNMENT_FORMAT = 'PIR' #######################ALIGNMENT FILE###################### >P1;1dz8 structureX:1dz8: 11 :A: 414 :A:undefined:undefined: 9.99: 9.99 -----LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIQRPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* >P1;2cpp structureX:2cpp: 10 : : 414 : :undefined:undefined: 1.63: 9.99 ----NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* ########################################################## Thanking you sridhar ------ End of Forwarded Message

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NOTE FOR BASH USERS
by Romain.Studer＠etu.unil.ch 01 May '03

01 May '03

NOTE FOR BASH USERS: I run modeller and it crashes with this message: "/bin/mod6v2: line 38: 1874 Segmentation fault (core dumped) $NICE ${EXECUTABLE} $STEERF >$LOGF" I used bash and I put the following command line in the .bashrc file as suggested in some messages of the mailing list: ulimit -S unlimited It appears that using the -s (lower case "s") solved the problem mentioned above. -S means Soft limitation and -s for stack maximum. The correct command is therefor: ulimit -s unlimited

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Restraints
by Anurag Sethi 29 Apr '03

29 Apr '03

Hi, I am modeling membrane proteins and I dont want a particular loop to enter in to the membrane. However as this loop is long (about 40 amino acids) and has nothing to model on (gap in template), it seems to form a sheet parallel to the transmembrane helices. This has to be avoided because the loop should not enter the membrane. My question is whether I can cause some restraints in Modeller by which any of the atoms in the loop donot have z-coordinate below a certain number. Thanks in advance, Anurag Sethi

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problem with files .top solve
by JP 24 Apr '03

24 Apr '03

when the files file.top or file.ali don`t have a last line in blank the process not run. always this files should have this last line in blank . thanks all.

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problem with files .top
by JP 24 Apr '03

24 Apr '03

(- suse linux 8.1 - modeller6v2 - file pdb is pdb1f4a.ent ) with file modelo1.top the process to run correctly INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'archivo.ali' SET KNOWNS = '1f4aC' SET SEQUENCE = 'sec1' SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' ----------------------------------------------------------------------------------------------------- BUT with file modelo2.top the process not run INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'archivo.ali' SET KNOWNS = '1f4aC' SET SEQUENCE = 'sec1' SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' and log file is: 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, Linux bioinf4 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/23 11:53:47.784 TOP_________> 105 705 SET ALNFILE = 'archivo.ali' TOP_________> 106 706 SET KNOWNS = '1f4aC' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET STARTING_MODEL = 1 TOP_________> 109 709 SET ENDING_MODEL = 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/23 11:53:47.784 Closing time : 2003/04/23 11:53:50.734 Total CPU time [seconds] : 2.88 ---------------------------------------------------------------------------------------- which is a problem? which is a difference between the files modelo1.top and modelo2.top? is a bug the modeller? the files top to contain the same information but with file model2.top the process not run. thanks..

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optimize with a membrane protein
by jxs818＠bham.ac.uk 24 Apr '03

24 Apr '03

Hi All I am trying to model an membrane protein, and wondered how to turn off the optimize routine for selected parts of the protein. What I am really after is for Modeller to just do the sidechain replacement in the membrane domain and then do its normal job (whichs its very good at!) in the more variable loop regions. Cheers all John

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Superposer two protein structure
by Shiyong Liu 23 Apr '03

23 Apr '03

Dear all, When I do superpose two proteins , I don't know how to output the structures of the two proteins totally. In the default superpose.top script, the output command is WRITE_MODEL2 FILE = '2ctx.fit' . I want to output two structures in one file at the same time so that I can display them easily in one windows. Best regards, Shiyong Peking University

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problem with check_alignment
by JP 21 Apr '03

21 Apr '03

- Suse linux 8.1 my files are: me Top File bioinf@bioinf4:/usr/local/bin/modeller6v2/work> more modelo.top 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 = '1f36A' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model (determines how many models tocalculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling the files: bioinf@bioinf4:/usr/local/bin/modeller6v2/work> ls -al total 188 drwxr-xr-x 2 bioinf users 216 2003-04-21 14:31 . drwxrwxrwx 5 wwwrun root 120 2003-04-21 14:28 .. -rw-r--r-- 1 bioinf users 281 2003-04-21 14:29 alignment.ali -rw-r--r-- 1 bioinf users 643 2003-04-21 14:31 modelo.top -rw-r--r-- 1 bioinf users 175446 2003-04-21 14:29 pdb1f36.ent log file 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, Linux bioinf4 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/21 14:31:58.119 TOP_________> 105 705 SET ALNFILE = 'alignment.ali' TOP_________> 106 706 SET KNOWNS = '1f36A' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/21 14:31:58.119 Closing time : 2003/04/21 14:32:01.072 Total CPU time [seconds] : 2.93 what is a problem?

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PSC Summer Workshop: Modeling from Protein Sequence to Structure
by Troy Wymore 21 Apr '03

21 Apr '03

Hello MODELLERs, The following workshop should be of interest to researchers subsribing to this list; especially those wanting to refine structures generated with MODELLER. *************************************************** PSC BIOMEDICAL INITIATIVE WORKSHOP 2003 MODELING FROM PROTEIN SEQUENCE TO STRUCTURE: COMPUTATIONAL TOOLS FOR STRUCTURE PREDICTION June 2-5 Application Deadline: April 30 Primary Instructor: Prof. Charles Brooks (Scripps) This workshop will introduce researchers to computational tools (the MMTSB Tool Set available at http://mmtsb.scripps.edu) aimed at predicting structure based on sequence alone, from identification of suitable homology templates, or through application of secondary-structure templated de novo folding, as well as refinement and energy calculations on "ensembles" of molecular structures. This freely available tool set comprises a perl-based library of applications that interface to the molecular modeling packages CHARMM and Amber, and the MONSSTER package for protein structure prediction. Participants in the workshop will be presented lectures on molecular modeling theory and practice, protein structure prediction, loop modeling and energy-based structure refinement. Advanced sampling methods such as replica-exchange molecular dynamics, as utilized in structure prediction algorithms, will be discussed. Practical tutorials exploring the use and application of the MMTSB tool set will focus on conventional molecular mechanics calculations of energy, minimization and dynamics as well as loop modeling and refinement using replica-exchange molecular dynamics and hierarchical protein structure prediction using de novo (or secondary structure templated) folding algorithms in the MONSSTER and CHARMM packages. Web-based servers for protein sequence alignment, secondary structure prediction and homology template identification will be discussed in the context of their utility to the overall structure prediction pipeline utilizing the MMTSB Tool Set. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/training/workshops/2003/proteomics/index.html If you have any questions, please contact Nancy Blankenstein at blankens(a)psc.edu

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