- modeller_usage - salilab.org

PDB problem
by Frederico Moreno 18 Jul '02

18 Jul '02

Hi, I'm using a correct pdb files. I got this message below. What's wrong? openf5__224_> Open 11 OLD SEQUENTIAL /home/pepeu/Modeller/modeller6v2/examples/Lectin/1h9p.pdb rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 237 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Moreno _______________________________________________________________________ Yahoo! Encontros O lugar certo para encontrar a sua alma gêmea. http://br.encontros.yahoo.com/

2 1

Alignment problem
by Frederico Moreno 18 Jul '02

18 Jul '02

Dear Bozidar, I had problem when trying to get some a protein model. What do I have to do? I used the PIR alignment format also. My Top file is: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.seg.pap' # alignment filename SET KNOWNS = '1h9p' # codes of the templates SET SEQUENCE = '1drg' # 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 The alignment file seems to be ok: Kind, OS, HostName, Kernel, Processor: 4, Linux localhost.localdomain 2.4.18-6mdkenterprise i686 Date and time of compilation : 07/05/2002 17:30:36 Job starting time (YY/MM/DD HH:MM:SS): 2002/07/18 13:08:16.425 TOP_________> 105 705 SET ALNFILE = 'alignment.seg.pap' TOP_________> 106 706 SET KNOWNS = '1h9p' TOP_________> 107 707 SET SEQUENCE = '1drg' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 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]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL alignment.seg.pap Dynamically allocated memory at amaxbnd [B,kB,MB]: 2560929 2500.907 2.442 openf5__224_> Open 11 OLD SEQUENTIAL alignment.seg.pap Read the alignment from file : alignment.seg.pap Total number of alignment positions: 0 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1h9p 0 1 2 1drg 0 1 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND 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]: 2560929 2500.907 2.442 Starting time : 2002/07/18 13:08:16.425 Closing time : 2002/07/18 13:08:17.598 Frederico Moreno _______________________________________________________________________ Yahoo! Encontros O lugar certo para encontrar a sua alma gêmea. http://br.encontros.yahoo.com/

2 1

What is de problem??
by Juan Palacios 16 Jul '02

16 Jul '02

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 sys_____214E> File probably does not exist. Perhaps you have to increase swap space size. Filename: 1026244802 Command : uname -rnsm > 1026244802 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 0 0.000 0.000 Starting time : 2002/07/09 16:00:02.767 Closing time : 2002/07/09 16:00:02.892 Total CPU time [seconds] : 0.09 Thanks

3 2

Fwd: modeller top files
by Bozidar Yerkovich 12 Jul '02

12 Jul '02

from one of our fellow MODELLERs... Can anyone help? B.. ---------- Forwarded Message ---------- Subject: modeller top files Date: Fri, 12 Jul 2002 12:17:13 +0100 From: "Rosh Karunaratne" <HIDDEN> To: bozidar(a)salilab.org thanks for your help last week Ive been reading through the online modeller manual (version6) and am having trouble creating the 'right' top file for my ali file that I have created. Below are two of the examples i have tried (both using the modeller manual) but when I run procheck on the last *.B9999 file I get heavy violations and bad contatcs between atoms. All I am interested in is creating the 'best model' within least violations etc Is there a pre-prepared top file that you know of that will do this task? Thanks for your help Rosh INCLUDE #rho1 SET ALNFILE = 'name.ali' SET HETATM_IO = on SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DO_LOOPS = '1' SET LOOP_STARTING_MODEL =1 SET LOOP_ENDING_MODEL= 25 SET LOOP_MD_LEVEL = 'refine_5' CALL ROUTINE = 'model' or SET ALNFILE = 'name.ali' SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 2 SET ENDING_MODEL = 2 CALL ROUTINE = 'very_fast' CALL ROUTINE = 'model' _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx -------------------------------------------------------

1 0

new user
by erase test 11 Jul '02

11 Jul '02

Dear All! I/m a new user of modeller , before a time ago, i made teh download of modeller 6v2 , and just now i installed in my computer , linux/redhat 6.2. in instalation i make all thing complete give the key and the all instalation it's ok!! when i go ro run a some example from tutorial, if i run initial.top all works but if i run compare.top i have a problems : TOP_________> 5 5 COMPARE OUTPUT = 'LONG' pdbnam__217W> Filename for PDB code not found: 1fdx.B99990001 Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL ./1fdx.atm openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found get_nal_378E> Error reading sequence from PDB file: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 i know that mean they can't found the file , why? the file are there, more question when i run a example from bin direcoty, they have a errors too: assgn___544E> Variable name not recognized: MAX_ITERATIONS_STORE Command line: SET MAX_ITERATIONS_STORE = MAX_ITERATIONS assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: ARGUMENTS Element, element type: REFINE_HOT_ONLY 3 Command line: IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN 'GO_TO __BEGIN_MD' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: VIOL_REP_STORE Command line: SET VIOL_REP_STORE = VIOL_REPORT_CUT assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: ARGUMENTS Element, element type: RSTRS_REFINED 3 Command line: IF ARGUMENTS = RSTRS_REFINED 0, OPERATION = 'EQ', T HEN 'SET VIOL_REPORT_CUT = 4 4 4 4 4 999 999 999 999 999 999 999 999 999 999 999 999 4 4 4 999 999 999 999 999 999 999 999 999 999 999' assgn___525E> Error in TOP variable assignment. and more, some one can exaplind me why i didn't get a normal anwser? i really dont want to run under by windows , i really dont have this type of machine ;-) and don't want best regads, -miki roit

1 0

complete set of execs for repaired 6v2
by Bozidar Yerkovich 09 Jul '02

09 Jul '02

Hi all, You can now access all 7 executables for the repaired 6v2, including windows version. >From now on there should be no MPAIRS errors/crashes. Happy modeling, Bozidar

1 0

the alignment problem
by Margot Ernst 08 Jul '02

08 Jul '02

thanks for all who replied to my original posting. The bottom line appears to be that various groups have been using a "user-driven" approach to iterative alignment - model optimization, but no generally recommended or automated protocol appears to be in use. thanks once more, margot

1 0

Some problems with respect to non-standard residues
by Kong Lesheng 08 Jul '02

08 Jul '02

It seems there are some differences with respect to non-standard residues between Modeller4 and Modeller6v2. I'm working on conotoxin. Some conotoxin sequences include non-standard residues. (such as 1OMC.pdb includes HYP) When I used Modeller4 before, I modified the template file("HETATM" into "ATOM "), then did alignment and modelling. The non-standard residues were read as "B". I'm currently using Modeller6v2. When I did the same things, these residues were read as "G". So the program always complain "the sequence is different with structure." Maybe a dirty solution is : modify the template file, delete surplus atoms, change the non-standard residue into standard residue. But non-standard residues are important for the function of conotoxin. Is there a better way to deal with non-standard residues? It seems that "SET HETATM_IO=ON" can not solve this problem. Thank you very much! With best regards, Kong Lesheng -- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6774 7149 Fax: (65)6778 2466

1 0

The sequence of template was wrongly read!
by Kong Lesheng 07 Jul '02

07 Jul '02

Hi, I'm currently using Modeller6v2. It is very strange that in the alignment, the sequence from the template is wrong. The 17th residue should be "NH2", c-terminal amidation. But in the alignment file, it is replaced by "G". I attached my top file and log file? Is there any mistake in it? Thank you very much! With best regards, Kong Lesheng -- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6774 7149 Fax: (65)6778 2466

1 0

E> Array too small. Increase MPAIRS, 6v2 executable update July 4th 2002.
by Bozidar Yerkovich 04 Jul '02

04 Jul '02

Hi all, Several of you reported the problem of MODELLER crashing with the following error: E> Array too small. Increase MPAIRS. It seems that all of those problems were due to the scaling factor in natm2mpairs function in MODELLER code. I have changed the value and tested it with those problematic top files. I hope that others will find it stable too. What you need to do if you had this problem: reinstall 6v2, that's the only solution, since the problem was in the source code. Sorry ;-( For advanced users: you only need to replace the "sick' executable with the "repaired" one from our web site, and put it in your {MODINSTALL6v2}/bin/modeller6v2/bin directory. If some of you still experience this problem please let me know. New executables will be available sometime later today. Happy modeling, Bozidar

1 1