- modeller_usage - salilab.org

prb encountered, plz help
by rathankar rao 24 Apr '05

24 Apr '05

i had to model a protein whose ali file, top file and the log files are present here. i couldnt model it and its always presenting some or the other errors plz help there was one problem in the pdb file,: a ligand cme under the name of the heteroatom, had a residue number as 91 , which was supposed to be a number for the aminoacid. the next residue thus continued from 92 and so on. so i changed the residue numbers by 1. i changed the ligand atom number also as 1191 instead of 91 so that it is distinguished from the other aminoacids. despite all these it dosent work. i have one more doubt , if at all the protein as many chains then how do i model it. what is the command which is used to model a protein with chains. plz explain with regadrs rathankar __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com >P1;1ocs structureX:1ocs:30:A:160:A:yhr: yeast:2.03:0.217 AEPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLP------SFHKRVSKVRRRYSDFEFFRKLIKEISML NHPKV----MVPHLPGKILLSN-------RFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVR-FIEAEKFV* >P1;yhr sequence:yhr:1: :149: :yhr: yeast: 2.00: -1.00 SINANFSFQKAHVSDCTIVNG-DHGTKFAVWRITVFLEPNLKAFAAKRESYKIQTYKRYSDFVRLRENLLTRIKT AKPEKLNCLQIPHLPPSVQWYSSWKYQEVNLNKDWLAKRQRGLEYFLNHIILNSSLVEMTKDILIQFLEPSKRV* # Fichier d'entree pour la procedure 'model' INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'yhr.ali' SET KNOWNS = '1ocs' # SET SEQUENCE = 'yhr' # SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL= 1 SET ENDING_MODEL= 1 CALL ROUTINE = 'model' MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 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, 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, WinME build 4114, TJAY-4, uni, x86 Family 6 Model 3 Stepping 0 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/04/25 20:21:56.690 TOP_________> 109 749 SET ALNFILE = 'yhr.ali' TOP_________> 110 750 SET KNOWNS = '1ocs' TOP_________> 111 751 SET SEQUENCE = 'yhr' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 CALL ROUTINE = 'model' TOP_________> 116 419 CALL ROUTINE = 'getnames' TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 121 538 SET ROOT_NAME = SEQUENCE TOP_________> 122 539 RETURN TOP_________> 123 420 CALL ROUTINE = 'homcsr' TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL yhr.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 2743707 2679.401 2.617 openf5__224_> Open 20 OLD SEQUENTIAL yhr.ali Read the alignment from file : yhr.ali Total number of alignment positions: 149 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ocs 131 1 1ocs yhr 2 yhr 148 1 yhr yhr TOP_________> 125 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 126 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1ocs Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2743857 2679.548 2.617 Starting time : 2004/04/25 20:21:56.690 Closing time : 2004/04/25 20:22:01.300 Total CPU time [seconds] : 4.61

2 1

Python interpreter with Modeller 8v0
by gerald.quon＠utoronto.ca 22 Apr '05

22 Apr '05

Hi, I'm trying to use basic python commands with modeller 8, but am finding the commands are simply ignored. I'm mainly interested in using the 'import' command so i can build a small library of functions for use with MODELLER scripts, but the import command doesn't seem to be working for me - has anyone tried it? If not, I'm wondering if it's possible to use a standard python interpreter for say, linux, instead of the MODELLER interpreter. Thanks! Gerald

2 1

potassium ion
by fredrik 18 Apr '05

18 Apr '05

Hi, I have a template with a potassium ion and I'm trying to use it in my modelling. What I can see from the manual and file code I should use: % in the .ali MK as atom name in the .pdb K as residue name in the .pdb ATOM instead of HETATM in the .pdb This how ever doesn't work. I have tried to use e.g. zinc ion and that work (z, ZN2, ZN2 resp.). I would be very great full for any help! Regards, Fredrik.

2 3

Modeller 8v0 release
by Modeller Caretaker 18 Apr '05

18 Apr '05

The new version of Modeller, 8v0, is now available for download from http://salilab.org/modeller/. If you have a license key for Modeller 7v7, there is no need to reregister for Modeller 8v0 - the same license key will work. (It won't do any harm to reregister if you want to, though!) If you encounter bugs in Modeller 8, please see http://salilab.org/modeller/manual/node11.html for information on how to report them. New features in Modeller 8 include: # TOP is no longer used as the scripting language. MODELLER now reads Python 2.3 scripts instead. (TOP scripts can still be used, but will not take advantage of all new features.) See Chapter 4 for more information. # Incorporation of the GA341 (model.assess_ga341()) and DOPE (model.assess_dope()) methods for model assessment. # `Automatic' filename generation (when filenames were set to 'default') is no longer supported; use the modfile.default() function instead. # Memory is used much more efficiently, and various limits evident in older releases (e.g., errors concerning MAXRES, MAXCNS and MAXBND) have been removed. Consequently, you can no longer assign to the MAXRES variable; this is not necessary now. # New alignment.salign() alignment command, using structural information, and based on the COMPARER program. # Various fixes to profile.build(), and a new command profile.scan(), for building and using sequence profiles. # Generated models can be docked to electron microscopy density maps, using the new density.grid_search() command. # Superpositions are now improved by using local substructures. This local refinement can be disabled (thus getting the behavior of old MODELLER versions) by turning off the refine_local option to model.superpose(). # MODELLER will now read compressed files in the .gz and .bz2 formats (as well as the existing .Z format) provided the gzip and bzip2 programs are available. # Fixes for various problems reading alignment files with very long lines, or with Mac, Unix or DOS-style line endings. # Bug fix for alignment.compare_structures(); disulfide bridges were not being properly considered in the comparison. # Charges for all topologies are now assigned using a `nearest neighbor' technique; see topology.make(). # sequence_db.search() (formerly SEQUENCE_SEARCH) now takes a 1-sequence alignment as input, rather than reading in that alignment itself. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

1 0

joining of the same domain
by rathankar rao 18 Apr '05

18 Apr '05

Dear sir i have a query protein of 300 residues which has 14 zinc finger binding motifs and each motif is not identically the same. i have a template which has 3 chains with each chain having only 87 residues, all the chains being identical. if i need to build a model to my query, i thought of chopping my query sequence in to three parts nearly such that each part resemble my template of 87 residues. it is seen that the sequence identity is nearly 50% for each part with the template. if i build models for these independent regions, 1. how do i join them. 2. how do i know their relative orientation and 3. how do i account for the dna which binds to it, plz explain. --------------------------------- Do you Yahoo!? Plan great trips with Yahoo! Travel: Now over 17,000 guides!

1 0

Modelling Hydrogen bond in helix
by Panapat Uawithya 17 Apr '05

17 Apr '05

Hi, I have generate a model. However the hydrogen bond distances in the helices are shorter than normal value eg. 2.5-2.9 Angstrom. The hydrogen bond of the template are in normal range 2.9-3.5 Angstrom. How can I correct this proble? I have tried energy minimaztion but distance come a little bit shorter. Panapat __________________________________ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail

1 0

(no subject)
by Michael Grabe 13 Apr '05

13 Apr '05

dear modellers, what should i do if i want the homology derived restraints to have a larger weight in the creation of a model. that is i want my model to look more like the template structure at the expense of stereochemical considerations. thanks, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

1 0

tutorial on mod7v7
by Paula R.=?ISO-8859-1?Q?_Kuser_Falc=E3o?= 11 Apr '05

11 Apr '05

Hi, I am trying to do the modeller tutorial on a linux machine, with version mod7v7. After running seq_search for the TvDLH model the seqsearch.dat is empty, and I get the .log file as shown below. Would you know why I can't get any answer from my search? Thanks, Paula. Kind, OS, HostName, Kernel, Processor: 4, Linux japiim.cbi.cnptia.embrapa.br 2.4.20-42.9.legacysmp i 686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/04/11 16:50:46.106 Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 100 TOP_________> 3 3 SET MAXRES = 300 TOP_________> 4 4 SET FILE = 'TvLDH.seq' TOP_________> 5 5 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Dynamically allocated memory at amaxseq [B,kB,MB]: 614337 599.938 0.586 Dynamically allocated memory at amaxbnd [B,kB,MB]: 32806393 32037.492 31.287 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.seq Searching a list of chains for similarity with a given sequence: Target sequence : TvLDH.seq List of test chains : ${MODINSTALL7v7}/modlib//CHAINS_3.0_40_XN.cod Number of test chains : 0 Residue-residue metric: ${MODINSTALL7v7}/modlib//as1.sim.mat Gap penalties U, V : -900.00 -50.00 Randomizations : 100 +/- range for sig2&3 : 10 SIGNIF_CUTOFF : 4.00 5.00 Top chains are listed : 20 (see the corresponding $MODINSTALL/modlib/seqfilt_*.grp file for more related PDB codes) RELATED_SEQUENCES # CODE_1 CODE_2 LEN1 LEN2 NID %ID %ID SCORE SIGNI SIGNI2 SIGNI3 ----------------------------------------------------------------------------- --- openf5__224_> Open 14 UNKNOWN SEQUENTIAL seqsearch.dat Dynamically allocated memory at finish [B,kB,MB]: 32806393 32037.492 31.287 Starting time : 2005/04/11 16:50:46.106 Closing time : 2005/04/11 16:50:46.882 Total CPU time [seconds] : 0.58 Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

problem!
by vivek sharma 09 Apr '05

09 Apr '05

Dear sir, Please have a look to this error. I made a normal modeller run (7v7) to generate 50 structures for a target sequence of about 500 residues using 3 different templates. But after generating 6 intial structure, it died with this following details, this log file was pretty big in size and contained this detail. I regularly use MODELER , but this a new kind of error I faced, what can be the reason? ---------------------- 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 Initial value of energy before optimization : ---------------- Current energy : ???????????????? Symmetry term within energy : 0.0000 Number of iterations : 200 Number of calls to energy function : 0 Number of updates of dynamic contacts : 5 Number of non-updates of dynamic contacts : 196 Final maximal atomic shift : ???????? TEMPERATURE : 150.000 EQUILIBRATE : 20 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.390 Maximal energy, step : ---------------- 0 Minimal energy, step : ???????????????? 200 Average energy, stand.dev. : ???????????????????????????????? Average atomic shift along one axis : ???????? MODEL returned : FINAL ------before this whole log file was filled up with this; -------------- ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? --------------- looks like some bond/bonds has gone too short and that might have affected the energy of system to go out of limits. But how can I found out which bond is that or some details like that? Hoping for a quick reply, Best regards, Vivek -- VIVEK SHARMA HBG BI "I never think of the future - it comes soon enough." A.Einstein

1 0

(no subject)
by Michael Grabe 08 Apr '05

08 Apr '05

dear modellers, i use the BUILD_MODEL command to introduce a mutation into a template structure, but I want to generate different rotomer conformations and get some kind of score for the trial without going through the entire "model" routine. I just want to look at very local rearrangements and not worry about the rest of the protein that is exactly the same. does anyone have any suggestions or test scripts that can help me with this. thanks a lot, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

1 0