- modeller_usage - salilab.org

[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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RE: RE:
by Eswar Narayanan 05 Feb '04

05 Feb '04

Absolutely! You have the solution right there! Account for the missing residue numbers of Mg/ATP in the alignment file. Modeller reads a PDB file as specified in the alignment format - so if you include more residues in the template, you have to alter the PIR format fields to tell the program to read them in from the PDB file first. Eswar. --- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar -----Original Message----- From: SLN Prasad Reddy [mailto:sreeyapu@rediffmail.com] Sent: Thursday, February 05, 2004 6:31 AM To: Eswar Narayanan Subject: Re: RE: Sir, I have given a mail a week back regarding modelling of hetero atoms along with main protein. You suggested me to check the number of residues in pdb file of template and .ali file. I checked it and it is same. I used fallowing .top file for modelling ( i am using modeller6v2 for windows nt) INCLUDE # Include the predefined TOP routines SET ALNFILE = 'fi.ali' # alignment filename SET KNOWNS = 'Tem11' # codes of the templates SET SEQUENCE = 'tar1' # code of the target SET MODEL_TOPOLOGY = 1 SET HYDROGEN_IO = off, HETATM_IO = on, WATER_IO = off SET TOPLIB = ${LIB}/top.lib SET PARLIB = ${LIB}/par.lib SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model #determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling Still the logfile is showing the number of residues in Pdb file of template and .ali are different and it also indicating the .ali file consists of 253 atoms and pdb file of template is having 251 ( The number of atoms present in my protein and template is 251 excluding heteroatoms.)So programme may be recognising Mg($) and ATP(@) in .ali file and not doing so with pdb dile of template. Kindly suggest me solution . Is the top file (above) i am using is a correct one for modelling hetatms. Thank you With regards Prasad. On Sat, 31 Jan 2004 Eswar Narayanan wrote : >Prasad, > > > >The error message tells you exactly what the problem is. The number of >residues in the alignment and PDB files are different. There are more or >less residues in the alignment than what is read in from the PDB file. > > > >Eswar. > > > >--- > >Eswar Narayanan, Ph.D > >Mission Bay Genentech Hall >600 16th Street, Suite N474Q >University of California, San Francisco >San Francisco, CA 94143-2240 (CA 94158 for courier) > >Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 > >http://www.salilab.org/~eashwar > >-----Original Message----- > From: SLN Prasad Reddy [mailto:sreeyapu@rediffmail.com] >Sent: Saturday, January 31, 2004 5:59 AM >To: eashwar(a)salilab.org >Subject: > > > > > Sir, > I am struggling in modeling a protein with ligand (ATP) and metal >atom (Mg). I am requesting you to help me in this regard. > > My problem : I want to model a protein with ligand and metal ion. >The template I have chosen is a crystal structure having both lignad and >metal atom. I tried with procedure given in the FAQ's question #16 of >Modeller6v2 manual . I found symbols for ATP and Mg form restyp.lib of >Modeller 6v2 and incorporated at the end of the alignment like following > > >P1;templ1 structureX:templ1:1::10:: >FAYVI/.$@* > >P1;targ1 sequence:targ1:1::8:: >-GWIV/.$@* > > >The top file is : > >INCLUDE >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ALNFILE = 'fi.ali' >SET KNOWNS = 'temp11' >SET SEQUENCE = 'targ1' >SET HETATM_IO = on >CALL ROUTINE = 'model' > > >But I am getting a log file as fallows > >TOP_________> 105 705 SET ALNFILE = 'fi.ali' > >TOP_________> 106 706 SET KNOWNS = 'temp11' > >TOP_________> 107 707 SET SEQUENCE = 'targ1' > >TOP_________> 108 708 SET HETATM_IO = ON > >TOP_________> 109 709 CALL ROUTINE = 'model' > >TOP_________> 110 399 CALL ROUTINE = 'getnames' > >TOP_________> 111 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', >OPERATION; > = 'EQ', THEN = 'STRING_OPERATE OPERATION = >CONCATENA; > TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' > >TOP_________> 112 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', >OPERATI; > ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = >CONCATE; > NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = >CSRFILE; > ' > >TOP_________> 113 511 STRING_OPERATE OPERATION = 'CONCATENATE', >; > STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = >SCHFILE > >TOP_________> 114 512 STRING_OPERATE OPERATION = 'CONCATENATE', >; > STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = >MATRIX_FI; > LE > >TOP_________> 115 513 SET ROOT_NAME = SEQUENCE > >TOP_________> 116 514 RETURN > >TOP_________> 117 400 CALL ROUTINE = 'homcsr' > >TOP_________> 118 106 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 fi.ali > >Dynamically allocated memory at amaxbnd [B,kB,MB]: 5865109 >5727.646 5.593 >openf5__224_> Open 11 OLD SEQUENTIAL fi.ali >read_al_374_> Non-standard residue type,position,sequence: $ 1 >read_al_374_> Non-standard residue type,position,sequence: @ 1 >read_al_374_> Non-standard residue type,position,sequence: $ 2 >read_al_374_> Non-standard residue type,position,sequence: @ 2 > >Read the alignment from file : fi.ali >Total number of alignment positions: > > # Code #_Res #_Segm PDB_code Name >--------------------------------------------------------------------------- - >--- > 1 temp11 1 temp11 > 2 targ1 1 targ1 >TOP_________> 119 107 CHECK_ALIGNMENT > >check_a_343_> >> BEGINNING OF COMMAND >openf5__224_> Open 11 OLD SEQUENTIAL ./temp11.pdb >rdabrk__290E> Number of residues in the alignment and pdb files are >different: > For alignment entry: 1 >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > >Dynamically allocated memory at finish [B,kB,MB]: 5865109 >5727.646 5.593 >Starting time : 2000/08/03 >19:06:47.190 >Closing time : 2000/08/03 >19:06:52.888 >Total CPU time [seconds] : 0.00 > > > Kindly suggest me a solution to my problem. > > >Thanking you > > >With regards > >Prasad . > > > > <http://clients.rediff.com/signature/track_sig.asp> > <http://clients.rediff.com/signature/track_sig.asp>

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big_sequence
by "Chupakhin - Чупахин" 02 Feb '04

02 Feb '04

Dear Modeller! I'm trying to align sequence that 1200 residues long, and that cause internal error. In old discussions forum (1998) I've find link to the executables to the long (more then 1000) sequnces, but the link is old(guitar.rockfeleller.edu/pub/modeller/*), could you post new one. Thanks a lot, Chupakhin Vladimir

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comparative modeling of protein
by Spero Manolatos 02 Feb '04

02 Feb '04

I have a 980 amino acid protein whose structure is unknown. I wish to learn if this protein belongs to a known family of protein of similar structure. I am not sure how to go about searching the modeler database to see if at least part of the sequence is similar to another sequence. Your help would be appreciated. S. Manolatos

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