Other STACK PROBLEMS and Re: [modeller_usage] Modeller 7v7 Stack problems, tried EVERYTHING!!!!
Dear all Modeller user,
I follow by so near this question and answers because I have the same error message.
I do the download of "Updated Windows binary" and I have the same problem of STACK OVERFLOW.
I do my example (top scripts) exactly as the example from Modeller basic tutorial avec my data, of course.
My sequence file is :
>P1;rpb3 sequence:rpb3:::::::0.00: 0.00 MVALTVEELTPEHIRFTLSNTTVGYANALRRILISEVPTIAIDMVEIERNNTVLPDEVLA HRLGLIPIYSKRELKYKEECSCSGFCSECSVVFEIDVVHTDDTLRTVSTRDIVCDEEDVI IKSGPVITKLARDQGLKARCIGRKGVGKTHAKWSPVSAISFEYDKDNVRRETNYWFEESI EEEWPGVRQGEANLMQKIDKIHMCVEVVEGGAGPLAVVLEGLRILKEKVATLSSAAETMD *
My script file is:
# Example to ALIGN RPB3 with the Template # # the template is 1i50C (pdb1i50.ent at C:\Program Files\Modeller7v7\examples\Testes\atom_files) # SET OUTPUT_CONTROL = 1 1 1 1 0
# directory with input atom files SET ATOM_FILES_DIRECTORY = './:../atom_files'
READ_MODEL FILE = 'pdb1i50.ent'
SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_FILES=ALIGN_CODES , ADD_SEQUENCE = on
READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_CODES 'rpb3'
ALIGN2D
WRITE_ALIGNMENT FILE='rpb3-1i50.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='rpb3-1i50.pap', ALIGNMENT_FORMAT = 'PAP'
I find an information at the FAQ messages that there are a Modeller's Variable called "MAXRES". I follow this suggestion from an modeller user: SET MAXRES=5000, and I did not get sucessful!!! but if I uses this ligne above:
SET MAXRES = 50000000
I have no 'stack overflow' error message but I have '_E> modeller error message (se the log file above)
Can you give some help ?
Many thanks.
My LOG file is :
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, WinXP build 2600 Service Pack 2, SANTOS, uni, x86 Family 15 Model 2 Stepping 9 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/24 12:06:44.218
TOP_________> 2 2 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 3 3 READ_MODEL FILE = 'pdb1i50.ent'
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent rdatm___297_> Segments, residues, atoms: 10 3558 28279 rdatm___298_> Segment: 1 2 A 1450 A 11154 rdatm___298_> Segment: 2 18 B 1224 B 8711 rdatm___298_> Segment: 3 3 C 268 C 2095 rdatm___298_> Segment: 4 1 E 215 E 1760 rdatm___298_> Segment: 5 72 F 155 F 679 rdatm___298_> Segment: 6 2 H 146 H 1068 rdatm___298_> Segment: 7 1 I 122 I 997 rdatm___298_> Segment: 8 1 J 65 J 532 rdatm___298_> Segment: 9 1 K 114 K 919 rdatm___298_> Segment: 10 25 L 70 L 364 TOP_________> 4 4 SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_F; ILES =ALIGN_CODES , ADD_SEQUENCE = ON
TOP_________> 5 5 SET MAXRES = 50000000
TOP_________> 6 6 READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_COD; ES 'rpb3'
openf5__224_> Open 20 OLD SEQUENTIAL rpb3.ali amaxres_215E> Dynamic memory allocation failed. Routine, variable, status: irestypn2 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2102291815 2053019.375 2004.902 Starting time : 2005/01/24 12:06:44.218 Closing time : 2005/01/24 12:08:38.125 Total CPU time [seconds] : 37.66
> Tom Petty wrote: > > I have a windows XP SP2 IBM laptop with plenty of memory (512MB > RAM) .... > >C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial >forrtl: severe (170): Program Exception - stack overflow > > > > This means that Modeller has exceeded the stack space limit. This a > constant, set when the Modeller binary was linked, so it won't help if > you add more memory to your machine. > ... > > Alternatively, you can download just such a 'fixed' binary from the > Modeller downloads page: > http://salilab.org/modeller/download_installation.html > (The link is right at the bottom: "Updated Windows binary".) > Use this binary to replace the existing mod7v7.exe file in your > Modeller installation (by default it should be in > C:\Program Files\modeller7v7\bin), and all should be well. > >If these problems persist, let me know. > > > Ben Webb, Modeller Caretaker >
Carlos Luiz N. dos SANTOS wrote: > I follow by so near this question and answers because I have the > same error message. > > I do the download of "Updated Windows binary" and I have the same > problem of STACK OVERFLOW.
The output you post does not contain a stack overflow error message; this is a different problem.
> I find an information at the FAQ messages that there are a > Modeller's Variable called "MAXRES". I follow this suggestion from an > modeller user: SET MAXRES=5000, and I did not get sucessful!!!
What error message do you see when you do that?
> SET MAXRES = 50000000
Did you try anything inbetween 5000 and 50000000? The latter is far too large.
> I have no 'stack overflow' error message but I have '_E> modeller > error message (se the log file above)
Just as the error message says, it's failed to allocate memory. This is because you've asked for far too much memory! Before it gave up, it had tried to allocate 2 gigabytes already...
Set MAXRES to something smaller. That value is too large.
Ben Webb, Modeller Caretaker
Dear all,
firstly I would like to thanks to all by tips and answers about my last problem of stack problems. Thanks!
I am using the basic tutorial steps (1., 2., 3. , 4. , 5.) to "modeling based on a single template" with my sequence data:
- I get sucessful at searching for structures related at my sequence (Step 1), No problems!
- I do the "STEP 2 - selecting a template" and I find it using the same tips from the tutorial. No problems again;
- The problems is in the 'STEP 3 - aligning with the template". Because I have just the target code at the _aln.pos columm and it is missing the template code and its data in the cbp20-1h2v.pap result file (in this message).
Why ??? I see the "align2d_276_> ALIGN_BLOCK changed to 1" message at log file (at end of this message) but I did not find the main raison for it. There are an template and a target. So I think the ALIGN-BLOCK is 2.
I used the TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib', but I am not sure that because there was not this command line at basic example. And if I run this script wihout this command line the Modeller tell me by warning that it missing in memory an topology library!
Can you help me ?
Best regards,
The cbp20-1h2v.pap result file is :
_aln.pos 10 20 30 40 50 60 cbp20 DHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNAR _consrvd
_aln.p 70 80 90 100 110 120 130 cbp20 NYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQV _consrvd
_aln.pos 140 150 160 170 180 190 200 cbp20 RRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCL _consrvd
_aln.pos 210 220 230 240 250 260 270 cbp20 WAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG _consrvd
_aln.pos 280 290 300 310 320 330 340 cbp20 PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHI _consrvd
_aln.pos 350 360 370 380 390 400 cbp20 DVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDC _consrvd
_aln.p 410 420 430 440 450 460 470 cbp20 LSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPSNPTCIYKYGDESSNSLPGHSVALCL _consrvd
_aln.pos 480 490 500 510 520 530 540 cbp20 AVAFKSKATNDEIFSILKDVPNFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKL _consrvd
_aln.pos 550 560 570 580 590 600 610 cbp20 HVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHV _consrvd
_aln.pos 620 630 640 650 660 670 680 cbp20 LKIQKELEEAKIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTPWYKNCIERLQ _consrvd
_aln.pos 690 700 710 720 730 740 cbp20 QIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA/EKLLKKSCTLYVGNLSFYTTEEQIY _consrvd
_aln.p 750 760 770 780 790 800 810 cbp20 ELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQY _consrvd
I have the follow sequence file:
>P1;cbp20 sequence:cbp20:::::::0.00: 0.00 MSLEEFDEVKYDHSTKRLDTPSRYLLRKARRNPNGLQELRESMKSSTIYVGNLSFYTSEE QIYELFSKCGTIKRIIMGLDRFKFTPCGFCFIIYSCPDEALNALKYLSDTKLDEKTITID LDPGFEDGRQFGRGKSGGQVSDELRFDFDASRGGFAIPFAERVGVPHSRFDNSSSQSNTN NYIPPPDAMGTFRPGFDEEREDDNYVPQ*
And my script file is :
SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = './:../atom_files' READ_MODEL FILE = '1H2V.pdb' READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib' SET ADD_SEQUENCE = on SEQUENCE_TO_ALI ALIGN_CODES = '1H2V' READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'cbp20', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='cbp20-1h2v.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='cbp20-1h2v.pap', ALIGNMENT_FORMAT = 'PAP'
And the LOG file is :
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, Linux santos.isima.fr 2.6.10-1.9_FC2 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/27 08:18:54.794
Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 3 3 READ_MODEL FILE = '1H2V.pdb'
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb
Dynamically allocated memory at amaxbnd [B,kB,MB]: 13862819 13537.909 13.221 openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb rdatm___297_> Segments, residues, atoms: 2 815 6667 rdatm___298_> Segment: 1 29 C 790 C 5905 rdatm___298_> Segment: 2 33 Z 125 Z 762 TOP_________> 4 4 READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_hea; v.lib'
openf5__224_> Open 11 OLD SEQUENTIAL /usr/lib/modeller7v7/modlib/top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 5 5 SET ADD_SEQUENCE = ON
TOP_________> 6 6 SEQUENCE_TO_ALI ALIGN_CODES = '1H2V'
TOP_________> 7 7 READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'c; bp20', ADD_SEQUENCE = ON
openf5__224_> Open 20 OLD SEQUENTIAL cbp20levure.ali openf5__224_> Open 20 OLD SEQUENTIAL cbp20levure.ali
Read the alignment from file : cbp20levure.ali Total number of alignment positions: 815
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 cbp20 815 2 1H2V undefined TOP_________> 8 8 ALIGN2D
Dynamically allocated memory at amaxbnd [B,kB,MB]: 31302189 30568.543 29.852 align2d_276_> ALIGN_BLOCK changed to 1. openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20
Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : ${MODINSTALL7v7}/modlib//as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 1000.0 2000.0 3000.0 4000.0 N_SUBOPT : 1 SUBOPT_OFFSET : 2.0000 Alignment block : 1 Gap introduction penalty : -900.0000 Gap extension penalty : -50.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 0.350 1.200 0.900 1.200 0.600 8.600 1.200 0.000 Length of alignment : 815 Score : -42490.0000 TOP_________> 9 9 WRITE_ALIGNMENT FILE ='cbp20-1h2v.ali', ALIGNMENT_FORMAT ; = 'PIR'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL cbp20-1h2v.ali TOP_________> 10 10 WRITE_ALIGNMENT FILE ='cbp20-1h2v.pap', ALIGNMENT_FORMAT ; = 'PAP'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL cbp20-1h2v.pap
Dynamically allocated memory at finish [B,kB,MB]: 31302189 30568.543 29.852 Starting time : 2005/01/27 08:18:54.794 Closing time : 2005/01/27 08:18:58.353 Total CPU time [seconds] : 3.47
Carlos Luiz N. dos SANTOS wrote: > I am using the basic tutorial steps (1., 2., 3. , 4. , 5.) to > "modeling based on a single template" with my sequence data: > > - I get sucessful at searching for structures related at my > sequence (Step 1), No problems! > > - I do the "STEP 2 - selecting a template" and I find it using > the same tips from the tutorial. No problems again; > > - The problems is in the 'STEP 3 - aligning with the template". > Because I have just the target code at the _aln.pos columm and it is > missing the template code and its data in the cbp20-1h2v.pap result file > (in this message). > > Why ??? I see the "align2d_276_> ALIGN_BLOCK changed to 1" > message at log file (at end of this message) but I did not find the > main raison for it. There are an template and a target. So I think the > ALIGN-BLOCK is 2.
No; ALIGN2D aligns two blocks of sequences with each other. ALIGN_BLOCK denotes the _last_ sequence in the _first_ block. So, with only two sequences, you want to align two blocks of one sequence each - so ALIGN_BLOCK should be 1.
> I used the TOPOLOGY FILE = > '/usr/lib/modeller7v7/modlib/top_heav.lib', but I am not sure that > because there was not this command line at basic example. And if I run > this script wihout this command line the Modeller tell me by warning > that it missing in memory an topology library!
You can read a topology file if you like, but that's not what's causing the problem in this case. Read on...
> SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ATOM_FILES_DIRECTORY = './:../atom_files' > READ_MODEL FILE = '1H2V.pdb' > READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib' > SET ADD_SEQUENCE = on > SEQUENCE_TO_ALI ALIGN_CODES = '1H2V' > READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'cbp20', > ADD_SEQUENCE = ON > ALIGN2D > WRITE_ALIGNMENT FILE='cbp20-1h2v.ali', ALIGNMENT_FORMAT = 'PIR' > WRITE_ALIGNMENT FILE='cbp20-1h2v.pap', ALIGNMENT_FORMAT = 'PAP'
You should change the READ_ALIGNMENT call to read: READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = ALIGN_CODES 'cbp20', ADD_SEQUENCE = ON
I notice the example in the tutorial is incorrect here too. (If you download the basic example .tar.gz, it's OK, but the align2d.top script at http://salilab.org/modeller/tutorial/basic.html was incorrect.) I've just corrected this.
Ben Webb, Modeller Caretaker
participants (2)
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Carlos Luiz N. dos SANTOS -
Modeller Caretaker