- modeller_usage - salilab.org

error in restraints calculation
by David Giganti 17 Feb '04

17 Feb '04

GOOD MORNING, MY MODELLER'S RUN WAS STOPPPED WHEN IT WAS CALCULATING THE RESTRAINS !!! SOMEBODY COULD EXPLAIN TO ME THE CAUSES OF THIS FAILURE. THANK YOU. r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 crsplin_459E> Increase MAXSPL to at least 1074 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 218439351 213319.700 208.320 Starting time : 2004/02/17 16:16:21.633 Closing time : 2004/02/17 16:18:53.259 Total CPU time [seconds] : 53.72

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Fortran Runtime Error
by Zoee Gokhale 15 Feb '04

15 Feb '04

Hi, Running MODELLER 6v2 on my Linux PCC (Red Hat 7.2) gives me the following error ? FORTRAN Runtime Error: ? Attempt to read past end of file ? READ(UNIT=11,... Please help me solve this problem. Thanks, Zoee Gokhale ___________________________________________________________ BT Yahoo! Broadband - Free modem offer, sign up online today and save £80 http://btyahoo.yahoo.co.uk

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[Mailman] request letter for vlarification of a doubt regarding modelling
by anthony johnson 12 Feb '04

12 Feb '04

dear sir, Iam a student of Bioinformatics and iam trying to do my protein modelling work on a tat protein of Hiv and from the 3DPSSM and my blast results i have found one template with good percentage of homology with my query. i retrieved the PDB of it to use it as the Atom file for submitting it to the modellor software that we have in our academic institute.But the problem was that the PDB was to be found as the NMR structure which was predicted to have 8 different models and the ID of the PDB is 1tvs and now iam in the confusion state that which model i have to choose as my atom file for submission to modellor software.Not only this hit, but most of my template hits are NMR structures and they too show me the same type of models.i came to view the site of modellor and i have found your mail ID , so iam mailing you my problem. And i humbly request you to show me a solution to this problem as i couldnt find any one who to help over here.hoping your kind favour in this regard. Awaiting your early reply. thanking you sir, Anthony Johnson anthony_johnson(a)rediffmail.com _______________________________________________ Mailman mailing list Mailman(a)salilab.org http://salilab.org/mailman/listinfo/mailman

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[modeller_usage] Request for a doubt clarification regarding modelling
by anthony johnson 12 Feb '04

12 Feb '04

Iam a student of Bioinformatics and iam trying to do my protein modelling work on a tat protein of Hiv and from the 3DPSSM and my blast results i have found one template with good percentage of homology with my query. i retrieved the PDB of it to use it as the Atom file for submitting it to the modellor software that we have in our academic institute.But the problem was that the PDB was to be found as the NMR structure which was predicted to have 8 different models and the ID of the PDB is 1tvs and now iam in the confusion state that which model i have to choose as my atom file for submission to modellor software.Not only this hit, but most of my template hits are NMR structures and they too show me the same type of models.i came to view the site of modellor and i have found your mail ID , so iam mailing you my problem. And i humbly request you to show me a solution to this problem as i couldnt find any one who to help over here.hoping your kind favour in this regard. Awaiting your early reply. thanking you sir, Anthony Johnson Yahoo! India Education Special: Study in the UK now.

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Re: [modeller_usage] divide__213E> Division by zero, during seq. search
by Esben Jannik Bjerrum 11 Feb '04

11 Feb '04

Well, your superstition isn't wrong, All characters needs to be UPPERCASE. Strange though that its halfway through the database that it fails when they are lowercase. Thanks for the help Esben

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COMMAND line clarification
by Nataraj Balkrishnan 10 Feb '04

10 Feb '04

Dear modeller, what is the significance of the line SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 in modeling top file ,what that command and associated number indicates. yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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divide__213E> Division by zero, during seq. search
by Esben Jannik Bjerrum 10 Feb '04

10 Feb '04

Dear modeller users. I'm currently blocked by an unusual problem. Running modeller for sequence search, it ends with a Divide__213E> Division by zero, error. I don't have a clue of whats wrong or where to start bugtracking. Hope that somebody can help me. Esben My NR2BS1S2.ali >P1;NR2BS1S2 sequence:NR2BS1S2:::::::0.00: 0.00 qeddhlsiVtleeapfvivesvdplsgtcmrntvpcqkrivtenktdeepgyikkcckgf cidilkkisksvkftydlylvtngkhgkkingtwngmigevvmkraymavgsltineers evvdfsvpfietgisvmvskgtqvsglsdkkfqrpndfsppfrfgtvpngsternirnny aemhaymgkfnqrgvddallslktgkldafiydaavlnymagrdegcklvtigsgkvfas tgygiaiqkdsgwkrqvdlailqlfgdgemeelealwltgichne* My seq_search.top #Modeller file SET SEARCH_RANDOMIZATIONS = 100 SEQUENCE_SEARCH FILE = 'NR2BS1S2.ali', ALIGN_CODES = 'NR2BS1S2', DATA_FILE = on last 55 lines of seq_search.log (7392993 bytes) seqsearc_> 3781 NR2BS1 1khhA 285 193 1 0.35 0.52 1718.00 _aln.pos 10 20 30 40 50 60 NR2BS1S2 --------------------qeddhlsiV- tleeapfvivesvdplsgtcmrntvpcqkrivtenktd 1khhA RWETPYMHSLAAAAASRGGR-------- VL-------------------------------------- _consrvd * _aln.p 70 80 90 100 110 120 130 NR2BS1S2 eepgyikkcckgfcidilkkisksvkftydlylvtngkhgkkingtwngmigevvmkraymavgslti 1khhA -------------------------------------------------------------------- _consrvd _aln.pos 140 150 160 170 180 190 200 NR2BS1S2 neersevvdfsvpfietgisvmvskgtqvsglsdkkfqrpndfs------------------------ 1khhA -------------------------------------------- EVGFGMAIAASRVQQAPIKEHWII _consrvd _aln.pos 210 220 230 240 250 260 270 NR2BS1S2 -------------------------------------------------------------------- 1khhA ECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAF _consrvd _aln.pos 280 290 300 310 320 330 340 NR2BS1S2 -------------------------------------------------------------------- 1khhA RLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAF _consrvd _aln.pos 350 360 370 380 390 400 NR2BS1S2 ----------- ppfrfgtvpngsternirnnyaemhaymgkfnqrgvddallslktgkldafiydaav 1khhA PQMITPLVTKH--------------------------------------------------------- _consrvd _aln.p 410 420 430 440 450 460 470 NR2BS1S2 lnymagrdegcklvtigsgkvfastgygiaiqkdsgwkrqvdlailqlfgdgemeelealwltgichn 1khhA -------------------------------------------------------------------- _consrvd _aln.pos NR2BS1S2 e 1khhA - _consrvd divide__213E> Division by zero; divisor = 0.0000 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 110299725 107714.578 105.190 Starting time : 2004/02/10 08:58:58.125 Closing time : 2004/02/10 09:11:00.162 Total CPU time [seconds] : 722.10

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How to get log file in windows
by Nataraj Balkrishnan 09 Feb '04

09 Feb '04

Dear modellers, I am doing my modelling of protein in modeller uder MS-DOS version ,the log information is visualized while I run my TOP script but could not be stored ,how can I retrive my log file after task been executed in window version of modeller. .. yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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RE: [modeller_usage] Modeller cant find .seq file
by Esben Jannik Bjerrum 09 Feb '04

09 Feb '04

Hi All I've solved my problem, I hope the font for the mail-list will show the difference in the following. SEQUENCE_SEARCH FILE = 'blbp.seq', ALIGN_CODES = 'blbp' is correct and work while SEQUENCE_SEARCH FILE = ´blbp.seq´, ALIGN_CODES = ´blbp´ is incorrect and doesn't work: ´ is not equal to '. I copied the line from a web-page and modified it to my needs, so there was probably some font-conversion issues. My keyboard can't even produce the character ´, while it can make ' and `. Esben

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Modeller cant find .seq file
by Esben Jannik Bjerrum 06 Feb '04

06 Feb '04

Dear fellow modeller users I'm new to modeller and have some trouble to get it running. it cant find the blbp.seq file. I've tried to switch to uppercase filenames, but in vain. below is the output from the terminal session. I'm running on linux mandrake 9.2 Hope you have ideas about what is wrong Esben [esben@computer tut3]$ ls blbp.seq BLBP.seq BLBP.SEQ search.log search.top search.top~ [esben@computer tut3]$ cat blbp.seq >P1;blbp sequence:blbp:::::::: VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEE TSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA* [esben@computer tut3]$ cat search.top SET OUTPUT_CONTROL = 1 1 1 1 2 SET SEARCH_RANDOMIZATIONS = 10 SEQUENCE_SEARCH FILE = ´blbp.seq´, ALIGN_CODES = ´blbp´ [esben@computer tut3]$ modeller search.top [esben@computer tut3]$ cat search.log 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 computer.dfuni.dk 2.4.22-10mdksmp i686 Date and time of compilation : 07/05/2002 17:30:36 Job starting time (YY/MM/DD HH:MM:SS): 2004/02/06 13:17:35.587 Status of dynamic memory allocation in routine: amaxseq Variable T L1 U1 L2 U2 L3 U3 Size Bytes --------------------------------------------------------------------------- iseqdb I 1 1 1 4 nseqdb I 1 1 1 4 seqdb S 1 1 1 1 1 4 codep S 1 1 1 20 ialn2 I 1 1 1 3 3 12 nresn2 I 1 3 3 12 irestypn2 I 1 1 1 3 3 12 invaln2 I 1 1 1 3 3 12 nsegmn2 I 1 3 3 12 iress1n2 I 1 30 1 3 90 360 iress2n2 I 1 30 1 3 90 360 resol2 R 1 3 3 12 rfactr2 R 1 3 3 12 caln2 S 1 1 1 3 3 3 ccaln2 S 1 1 1 3 3 3 alnchn2 S 1 2 1 3 6 6 prottyp2 S 1 3 3 240 source2 S 1 3 3 240 range2 S 1 2 1 3 6 30 name2 S 1 3 3 240 segidn2 S 1 30 1 3 90 1800 codein2 L 1 3 3 12 iattmod I 1 50 50 200 iatmgrp I 1 220 220 880 grpatm S 1 50 50 250 attmod S 1 220 220 1980 var R 1 3 1 16 48 192 pdf R 1 3 1 50 150 600 ientry I 1 4 4 16 jentry I 1 4 4 16 nentries I 1 1 1 4 iar I 1 1 1 4 jar I 1 1 1 4 kar I 1 1 1 4 lar I 1 1 1 4 b1ic R 1 1 1 4 b2ic R 1 1 1 4 t1ic R 1 1 1 4 t2ic R 1 1 1 4 pic R 1 1 1 4 tar L 1 1 1 4 xmin R 1 1 1 4 ymin R 1 1 1 4 zmin R 1 1 1 4 ialn I 1 1 1 3 3 12 nresn I 1 3 3 12 irestypn I 1 1 1 3 3 12 invaln I 1 1 1 3 3 12 nsegmn I 1 3 3 12 iress1n I 1 30 1 3 90 360 iress2n I 1 30 1 3 90 360 resol R 1 3 3 12 rfactr R 1 3 3 12 alnacc R 1 1 1 4 prof R 1 1 1 4 4 16 gapdst R 1 3 1 3 9 36 caln S 1 1 1 3 3 3 ccaln S 1 1 1 3 3 3 alnchn S 1 2 1 3 6 6 prottyp S 1 3 3 240 source S 1 3 3 240 range S 1 2 1 3 6 30 name S 1 3 3 240 segidn S 1 30 1 3 90 1800 atmfull S 1 3 3 768 codein L 1 3 3 12 iresatmn I 1 1 1 3 3 12 natmn I 1 3 3 12 iatmr1n I 1 1 1 3 3 12 idih I 1 1 1 9 1 3 27 108 idihc I 1 1 1 9 1 3 27 108 iglbsim I 1 3 1 3 9 36 isstruc I 1 1 1 3 3 12 neigh I 1 1 1 3 3 12 ineigh I 1 50 1 1 1 3 150 600 iresol I 1 3 3 12 indats2n I 1 2 1 1 1 3 6 24 imnchw I 1 1 1 3 3 12 iacont I 1 3 3 12 idsta1 I 1 1 1 3 3 12 idsta2 I 1 1 1 3 3 12 fractglsim R 1 3 1 3 9 36 xn R 1 1 1 3 3 12 yn R 1 1 1 3 3 12 zn R 1 1 1 3 3 12 dih R 1 1 1 9 1 3 27 108 acc R 1 1 1 3 3 12 bison R 1 1 1 3 3 12 curvn R 1 1 1 3 3 12 atmnamn S 1 1 1 3 3 12 resnumn S 1 1 1 3 3 15 resnamn S 1 1 1 3 3 12 chainn S 1 1 1 3 3 3 accepts L 1 3 3 12 memrange S 1 2 1 6 1 3 36 36 memalnchn S 1 2 1 6 1 3 36 36 mematmfull S 1 6 1 3 18 4608 iatc I 1 5 1 1 5 20 natc I 1 1 1 4 iata I 1 3 1 1 3 12 iatd I 1 4 1 1 4 16 iatb I 1 2 1 1 2 8 iati I 1 4 1 1 4 16 resseg S 1 1 1 4 iatmr1 I 1 1 1 4 iattyp I 1 1 1 4 iresatm I 1 1 1 4 iatta I 1 1 1 4 indats I 1 1 1 3 3 12 irestyp I 1 1 1 4 idihres I 1 4 1 9 1 1 36 144 natngh I 1 1 1 4 radii R 1 1 1 4 charge R 1 1 1 4 x R 1 1 1 4 y R 1 1 1 4 z R 1 1 1 4 biso R 1 1 1 4 vx R 1 1 1 4 vy R 1 1 1 4 vz R 1 1 1 4 atmacc R 1 1 1 4 resnam S 1 1 1 4 atmnam S 1 1 1 4 resnum S 1 1 1 5 chain S 1 1 1 1 picres L 1 1 1 3 3 12 picatm L 1 1 1 3 3 12 katmr1 I 1 1 1 4 kresatm I 1 1 1 4 krestyp I 1 1 1 4 x2 R 1 1 1 4 y2 R 1 1 1 4 z2 R 1 1 1 4 charg2 R 1 1 1 4 biso2 R 1 1 1 4 radii2 R 1 1 1 4 atm2nam S 1 1 1 4 res2nam S 1 1 1 4 chain2 S 1 1 1 1 res2num S 1 1 1 5 dvx R 1 1 1 4 dvy R 1 1 1 4 dvz R 1 1 1 4 pdbfil S 1 16331 16331 2090368 pdblst S 1 16331 16331 81655 indatm I 1 1 1 4 itcsr I 1 7 1 1 7 28 iatm I 1 1 1 4 ipcsr I 1 1 1 4 indatt I 1 1 1 4 itacsr I 1 7 1 1 7 28 iatt I 1 1 1 4 ipacsr I 1 1 1 4 iapairs I 1 2 1 1 2 8 iarsr2 I 1 50 1 50 2500 10000 iarsr I 1 50 50 200 indcsr I 1 1 1 4 pcsr R 1 1 1 4 pacsr R 1 1 1 4 iatsym1 I 1 1 1 4 iatsym2 I 1 1 1 4 wghsym R 1 1 1 4 Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483 2148.909 2.099 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 10 TOP_________> 3 3 SEQUENCE_SEARCH FILE = ´BLBP.SEQ´, ALIGN_CODES = ´BLBP´ fullfn__230E> File not found: ´BLBP.SEQ´ Directories: Extensions : :.chn Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2004/02/06 13:17:35.587 Closing time : 2004/02/06 13:17:36.236 Total CPU time [seconds] : 0.65 [esben@computer tut3]$

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