- modeller_usage - salilab.org

Adding ligands to my MODEL
by Troy Wymore 15 Nov '02

15 Nov '02

Hello MODELLERs, I'm trying to add NAD to my modeled protein and keep getting a few errors, like: Atom index is out of bounds: 7002 7000 NAD is in ./modlib/top_heav.lib and I have added the symbol "J" to ./modlib/restyp.lib so that NAD can be recognized in my alignment file. NAD is in my TEMPLATE pdb file and alignment file. Does anyone have an example alignment and corresponding PDB file that they used to construct ligands along with the protein model? I expect that I'm missing something minor and an example would help. Many thanks, Troy Wymore Pittsburgh Supercomputing Center

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postdocs
by Andras Fiser 14 Nov '02

14 Nov '02

Dear All, I am setting up a lab in New York and looking for post docs and research associates/scientific programmers. If someone is interested, should follow this link for details: http://salilab.org/~andras/ad.html thanks, Andras -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Heteroatom problem solved
by John T. Penniston 13 Nov '02

13 Nov '02

1 0

tetrameric protein
by bharat adkar 13 Nov '02

13 Nov '02

hi, my protein is a homotetramer and also contains a metal ion per monomer. can i use it for homology modeling, either as template or target... BHARAT _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians

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electrostatic potential
by Yang Xiaolin 12 Nov '02

12 Nov '02

Hi all, I want to know where I can get softwares to calculate the electrostatic potential. Thanks Xiaolin

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error: Structure not read in
by Dr. Dan White 11 Nov '02

11 Nov '02

Hi All, I am a newbie to Modeller, and am having a problem reading in my template files in the log I get the error message: 3 lines just before the end bit..... check_a_343_> >> BEGINNING OF COMMAND check_a_347E> Structure not read in: 1 recover____E> ERROR_STATUS >=STOP_ON_ERROR: 1 1 All my files (.ali .top .atm .log) are shown below The 8 template files are in fact all the same (so I just show 1) , just with different filenames, to model different bits of the query sequence. They are called t2avi1.atm t2avi2.atm ..... t2avi8.atm I specify which of the 4 chains in the template files to use in the PIR alignment file in the 4th and 6th fields of the 2nd lines. My .top script file, .atm template files, and .ali PIR alignment file are all in /home/model/henri/ # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'avi4.ali' # alignment filename SET ALIGNMENT_FORMAT = 'PIR' #sets alignment format SET KNOWNS = 't2avi1' 't2avi2' 't2avi3' 't2avi4' 't2avi5' 't2avi6' 't2avi7' 't2avi8' # codes of the templates SET SEQUENCE = 'avi4' # code of the target SET ATOM_FILES_DIRECTORY = '/home/model/henri' # 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 >P1;2avi1 structureX:2avi1:3 :A:123 :A:::: -----------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIK ESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND IGDDWKATRVGINIFTRL------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------------------* >P1;2avi2 structureX:t2avi2:3 :A:123 :A:::: ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTG TYTTAVTATSNEIKESPLHGTENTINK--------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------RTQPTFGF TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >P1;2avi3 structureX:t2avi3:3 :D:123 :D:::: KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK---- ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------RTQPTFGFTVNWKFSESTTVFTGQCFI DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL---------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------------------* >P1;2avi4 structureX:t2avi4:3 :D:123 :D:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------------KCSLTGKWT NDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWK FSE--------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------STTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >P1;2avi5 structureX:t2avi5:3 :C:123 :C:::: KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK---- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV NDIGDDWKATRVGINIFTRL---------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------------------* >P1;2avi6 structureX:t2avi6:3 :C:123 :C:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEF TGTYTTAVTATSNEIKESPLHGTENTINK------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------RTQPTFGF TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >P1;2avi7 structureX:t2avi7:3 :B:123 :B:::: KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQP TFGFTVNWKFSES----------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL--- ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------------------* >P1;2avi8 structureX:t2avi8:3 :B:123 :B:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHG TENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWK ATRVGINIFTRL---------------------------------------------* >P1;avi4 sequence:avi4:1 : :554 : :::: ------------------------------------------------------------ -------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND IGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEFTG TYTTAVTATSNEIKESPLHGTQNTINK-SGGS------------------TTVFTGQCFI DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWD NDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWK FSEGGSGSGSGSGSGRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV NDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEF TGTYTTAVTATSNEIKESPLHGTQNTINKSGGS--------------------------- ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQ KEGGSGGSAR-KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHG TQNTINKRTQPTFGFTVNWKFSE------------------------------------- ---------------------------------------------------------* HEADER BIOTIN BINDING PROTEIN 23-APR-93 2AVI 2AVI 2 REMARK this now a tetramer, created with o, on sunday 22 sept 1996 REMARK by rik wierenga from 2avi.brk COMPND AVIDIN COMPLEX WITH BIOTIN 2AVI 3 SOURCE HEN EGG-WHITE 2AVI 4 AUTHOR O.LIVNAH,J.SUSSMAN 2AVI 5 REVDAT 1 15-JUL-93 2AVI 0 2AVI 6 REMARK 1 2AVI 7 REMARK 1 REFERENCE 1 2AVI 8 REMARK 1 AUTH O.LIVNAH,E.A.BAYER,M.WILCHEK,J.L.SUSSMAN 2AVI 9 REMARK 1 TITL THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE 2AVI 10 REMARK 1 TITL 2 AVIDIN-BIOTIN COMPLEX 2AVI 11 REMARK 1 REF PROC.NAT.ACAD.SCI.USA V. 90 5076 1993 2AVI 12 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 040 2AVI 13 REMARK 2 2AVI 14 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. 2AVI 15 REMARK 3 2AVI 16 REMARK 3 REFINEMENT. 2AVI 17 REMARK 3 PROGRAM XPLOR 2AVI 18 REMARK 3 AUTHORS BRUNGER 2AVI 19 REMARK 3 R VALUE 0.151 2AVI 20 REMARK 3 RMSD BOND DISTANCES 0.013 ANGSTROMS 2AVI 21 REMARK 3 RMSD BOND ANGLE 1.83 DEGREES 2AVI 22 REMARK 4 2AVI 23 REMARK 4 IN EACH MONOMER OF AVIDIN, RESIDUES 1 - 2 AND 124 - 128 2AVI 24 REMARK 4 ARE NOT INCLUDED IN THE ATOM LIST SINCE THE ELECTRON 2AVI 25 REMARK 4 DENSITY IS POOR IN THOSE REGIONS. 2AVI 26 REMARK 5 2AVI 27 REMARK 5 RESIDUE 34 OF EACH CHAIN EXISTS IN TWO FORMS - THR OR ILE. 2AVI 28 REMARK 5 IN THIS ENTRY IT IS PRESENTED AS THR. 2AVI 29 SEQRES 1 A 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP 2AVI 30 SEQRES 2 A 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG 2AVI 31 SEQRES 3 A 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA 2AVI 32 SEQRES 4 A 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR 2AVI 33 SEQRES 5 A 128 GLU ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY 2AVI 34 SEQRES 6 A 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL 2AVI 35 SEQRES 7 A 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU 2AVI 36 SEQRES 8 A 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN 2AVI 37 SEQRES 9 A 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE 2AVI 38 SEQRES 10 A 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU 2AVI 39 SEQRES 1 B 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP 2AVI 40 SEQRES 2 B 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG 2AVI 41 SEQRES 3 B 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA 2AVI 42 SEQRES 4 B 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR 2AVI 43 SEQRES 5 B 128 GLU ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY 2AVI 44 SEQRES 6 B 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL 2AVI 45 SEQRES 7 B 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU 2AVI 46 SEQRES 8 B 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN 2AVI 47 SEQRES 9 B 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE 2AVI 48 SEQRES 10 B 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU 2AVI 49 HET BTN A 150 16 BIOTIN 2AVI 50 HET NAG A 340 14 N-ACETYL-D-GLUCOSAMINE 2AVI 51 HET BTN B 150 16 BIOTIN 2AVI 52 HET NAG B 341 14 N-ACETYL-D-GLUCOSAMINE 2AVI 53 FORMUL 3 BTN 2(C10 H16 N2 O3 S1) 2AVI 54 FORMUL 4 NAG 2(C8 H15 N1 O5) 2AVI 55 FORMUL 5 HOH *74(H2 O1) 2AVI 56 CRYST1 72.150 80.370 43.540 90.00 90.00 90.00 C 21 21 2 8 2AVI 57 ORIGX1 1.000000 0.000000 0.000000 0.00000 2AVI 58 ORIGX2 0.000000 1.000000 0.000000 0.00000 2AVI 59 ORIGX3 0.000000 0.000000 1.000000 0.00000 2AVI 60 SCALE1 0.013860 0.000000 0.000000 0.00000 2AVI 61 SCALE2 0.000000 0.012442 0.000000 0.00000 2AVI 62 SCALE3 0.000000 0.000000 0.022967 0.00000 2AVI 63 ATOM 1 N LYS A 3 -2.040 13.882 -0.329 1.00 28.24 2AVI 64 ATOM 2 CA LYS A 3 -2.951 14.933 0.253 1.00 28.81 2AVI 65 ATOM 3 C LYS A 3 -2.548 15.170 1.710 1.00 26.30 2AVI 66 ATOM 4 O LYS A 3 -2.067 14.247 2.374 1.00 26.95 2AVI 67 ATO,,,,,, and so on 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 modeling.bio.jyu.fi 2.4.18-14 i686 Date and time of compilation : 07/05/2002 17:08:33 Job starting time (YY/MM/DD HH:MM:SS): 2002/11/08 20:34:11.701 TOP_________> 105 705 SET ALNFILE = 'avi4.ali' TOP_________> 106 706 SET ALIGNMENT_FORMAT = 'PIR' TOP_________> 107 707 SET KNOWNS = 't2avi1' 't2avi2' 't2avi3' 't2avi4' 't2avi; 5' 't2avi6' 't2avi7' 't2avi8' TOP_________> 108 708 SET SEQUENCE = 'avi4' TOP_________> 109 709 SET ATOM_FILES_DIRECTORY = '/home/model/henri' TOP_________> 110 710 SET STARTING_MODEL = 1 TOP_________> 111 711 SET ENDING_MODEL = 1 TOP_________> 112 712 CALL ROUTINE = 'model' TOP_________> 113 399 CALL ROUTINE = 'getnames' TOP_________> 114 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 115 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 116 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 117 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 118 513 SET ROOT_NAME = SEQUENCE TOP_________> 119 514 RETURN TOP_________> 120 400 CALL ROUTINE = 'homcsr' TOP_________> 121 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE 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 11 11 44 nresn2 I 1 11 11 44 irestypn2 I 1 1 1 11 11 44 invaln2 I 1 1 1 11 11 44 nsegmn2 I 1 11 11 44 iress1n2 I 1 30 1 11 330 1320 iress2n2 I 1 30 1 11 330 1320 resol2 R 1 11 11 44 rfactr2 R 1 11 11 44 caln2 S 1 1 1 11 11 11 ccaln2 S 1 1 1 11 11 11 alnchn2 S 1 2 1 11 22 22 prottyp2 S 1 11 11 880 source2 S 1 11 11 880 range2 S 1 2 1 11 22 110 name2 S 1 11 11 880 segidn2 S 1 30 1 11 330 6600 codein2 L 1 11 11 44 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 11 1 16 176 704 pdf R 1 11 1 50 550 2200 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 11 11 44 nresn I 1 11 11 44 irestypn I 1 1 1 11 11 44 invaln I 1 1 1 11 11 44 nsegmn I 1 11 11 44 iress1n I 1 30 1 11 330 1320 iress2n I 1 30 1 11 330 1320 resol R 1 11 11 44 rfactr R 1 11 11 44 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 11 11 11 ccaln S 1 1 1 11 11 11 alnchn S 1 2 1 11 22 22 prottyp S 1 11 11 880 source S 1 11 11 880 range S 1 2 1 11 22 110 name S 1 11 11 880 segidn S 1 30 1 11 330 6600 atmfull S 1 11 11 2816 codein L 1 11 11 44 iresatmn I 1 1 1 11 11 44 natmn I 1 11 11 44 iatmr1n I 1 1 1 11 11 44 idih I 1 1 1 9 1 11 99 396 idihc I 1 1 1 9 1 11 99 396 iglbsim I 1 11 1 11 121 484 isstruc I 1 1 1 11 11 44 neigh I 1 1 1 11 11 44 ineigh I 1 50 1 1 1 11 550 2200 iresol I 1 11 11 44 indats2n I 1 2 1 1 1 11 22 88 imnchw I 1 1 1 11 11 44 iacont I 1 11 11 44 idsta1 I 1 1 1 11 11 44 idsta2 I 1 1 1 11 11 44 fractglsim R 1 11 1 11 121 484 xn R 1 1 1 11 11 44 yn R 1 1 1 11 11 44 zn R 1 1 1 11 11 44 dih R 1 1 1 9 1 11 99 396 acc R 1 1 1 11 11 44 bison R 1 1 1 11 11 44 curvn R 1 1 1 11 11 44 atmnamn S 1 1 1 11 11 44 resnumn S 1 1 1 11 11 55 resnamn S 1 1 1 11 11 44 chainn S 1 1 1 11 11 11 accepts L 1 11 11 44 memrange S 1 2 1 6 1 11 132 132 memalnchn S 1 2 1 6 1 11 132 132 mematmfull S 1 6 1 11 66 16896 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]: 2239219 2186.737 2.135 openf5__224_> Open 11 OLD SEQUENTIAL avi4.ali Status of dynamic memory allocation in routine: amaxbnd 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 1 807 1 11 8877 35508 nresn2 I 1 11 11 44 irestypn2 I 1 807 1 11 8877 35508 invaln2 I 1 807 1 11 8877 35508 nsegmn2 I 1 11 11 44 iress1n2 I 1 30 1 11 330 1320 iress2n2 I 1 30 1 11 330 1320 resol2 R 1 11 11 44 rfactr2 R 1 11 11 44 caln2 S 1 807 1 11 8877 8877 ccaln2 S 1 807 1 11 8877 8877 alnchn2 S 1 2 1 11 22 22 prottyp2 S 1 11 11 880 source2 S 1 11 11 880 range2 S 1 2 1 11 22 110 name2 S 1 11 11 880 segidn2 S 1 30 1 11 330 6600 codein2 L 1 11 11 44 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 11 1 16 176 704 pdf R 1 11 1 50 550 2200 ientry I 1 309888 309888 1239552 jentry I 1 309888 309888 1239552 nentries I 1 77472 77472 309888 iar I 1 38736 38736 154944 jar I 1 38736 38736 154944 kar I 1 38736 38736 154944 lar I 1 38736 38736 154944 b1ic R 1 38736 38736 154944 b2ic R 1 38736 38736 154944 t1ic R 1 38736 38736 154944 t2ic R 1 38736 38736 154944 pic R 1 38736 38736 154944 tar L 1 38736 38736 154944 xmin R 1 9684 9684 38736 ymin R 1 9684 9684 38736 zmin R 1 9684 9684 38736 ialn I 1 807 1 11 8877 35508 nresn I 1 11 11 44 irestypn I 1 807 1 11 8877 35508 invaln I 1 807 1 11 8877 35508 nsegmn I 1 11 11 44 iress1n I 1 30 1 11 330 1320 iress2n I 1 30 1 11 330 1320 resol R 1 11 11 44 rfactr R 1 11 11 44 alnacc R 1 807 807 3228 prof R 1 807 1 4 3228 12912 gapdst R 1 809 1 809 654481 2617924 caln S 1 807 1 11 8877 8877 ccaln S 1 807 1 11 8877 8877 alnchn S 1 2 1 11 22 22 prottyp S 1 11 11 880 source S 1 11 11 880 range S 1 2 1 11 22 110 name S 1 11 11 880 segidn S 1 30 1 11 330 6600 atmfull S 1 11 11 2816 codein L 1 11 11 44 iresatmn I 1 9684 1 11 106524 426096 natmn I 1 11 11 44 iatmr1n I 1 807 1 11 8877 35508 idih I 1 807 1 9 1 11 79893 319572 idihc I 1 807 1 9 1 11 79893 319572 iglbsim I 1 11 1 11 121 484 isstruc I 1 807 1 11 8877 35508 neigh I 1 807 1 11 8877 35508 ineigh I 1 50 1 807 1 11 443850 1775400 iresol I 1 11 11 44 indats2n I 1 2 1 9684 1 11 213048 852192 imnchw I 1 807 1 11 8877 35508 iacont I 1 11 11 44 idsta1 I 1 807 1 11 8877 35508 idsta2 I 1 807 1 11 8877 35508 fractglsim R 1 11 1 11 121 484 xn R 1 9684 1 11 106524 426096 yn R 1 9684 1 11 106524 426096 zn R 1 9684 1 11 106524 426096 dih R 1 807 1 9 1 11 79893 319572 acc R 1 807 1 11 8877 35508 bison R 1 9684 1 11 106524 426096 curvn R 1 807 1 11 8877 35508 atmnamn S 1 9684 1 11 106524 426096 resnumn S 1 807 1 11 8877 44385 resnamn S 1 807 1 11 8877 35508 chainn S 1 807 1 11 8877 8877 accepts L 1 11 11 44 memrange S 1 2 1 6 1 11 132 132 memalnchn S 1 2 1 6 1 11 132 132 mematmfull S 1 6 1 11 66 16896 iatc I 1 5 1 9684 48420 193680 natc I 1 9684 9684 38736 iata I 1 3 1 19368 58104 232416 iatd I 1 4 1 29052 116208 464832 iatb I 1 2 1 9684 19368 77472 iati I 1 4 1 4035 16140 64560 resseg S 1 807 807 3228 iatmr1 I 1 807 807 3228 iattyp I 1 9684 9684 38736 iresatm I 1 9684 9684 38736 iatta I 1 9684 9684 38736 indats I 1 9684 1 3 29052 116208 irestyp I 1 807 807 3228 idihres I 1 4 1 9 1 807 29052 116208 natngh I 1 9684 9684 38736 radii R 1 9684 9684 38736 charge R 1 9684 9684 38736 x R 1 9684 9684 38736 y R 1 9684 9684 38736 z R 1 9684 9684 38736 biso R 1 9684 9684 38736 vx R 1 9684 9684 38736 vy R 1 9684 9684 38736 vz R 1 9684 9684 38736 atmacc R 1 9684 9684 38736 resnam S 1 807 807 3228 atmnam S 1 9684 9684 38736 resnum S 1 807 807 4035 chain S 1 807 807 807 picres L 1 807 1 3 2421 9684 picatm L 1 9684 1 3 29052 116208 katmr1 I 1 807 807 3228 kresatm I 1 9684 9684 38736 krestyp I 1 807 807 3228 x2 R 1 9684 9684 38736 y2 R 1 9684 9684 38736 z2 R 1 9684 9684 38736 charg2 R 1 9684 9684 38736 biso2 R 1 9684 9684 38736 radii2 R 1 9684 9684 38736 atm2nam S 1 9684 9684 38736 res2nam S 1 807 807 3228 chain2 S 1 807 807 807 res2num S 1 807 807 4035 dvx R 1 9684 9684 38736 dvy R 1 9684 9684 38736 dvz R 1 9684 9684 38736 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 9684 9684 38736 iatsym2 I 1 9684 9684 38736 wghsym R 1 9684 9684 38736 Dynamically allocated memory at amaxbnd [B,kB,MB]: 18672759 18235.120 17.808 openf5__224_> Open 11 OLD SEQUENTIAL avi4.ali Read the alignment from file : avi4.ali Total number of alignment positions: 554 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 t2avi1 0 1 2 t2avi2 0 1 3 t2avi3 0 1 4 t2avi4 0 1 5 t2avi5 0 1 6 t2avi6 0 1 7 t2avi7 0 1 8 t2avi8 0 1 9 avi4 554 1 avi4 TOP_________> 122 107 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]: 18672759 18235.120 17.808 Starting time : 2002/11/08 20:34:11.701 Closing time : 2002/11/08 20:34:15.869 Total CPU time [seconds] : 2.25 dan(a)chalkie.org.uk http://www.chalkie.org.uk Daniel James White PhD. Cell Biology Department of Biological and Environmental Science University of Jyväskylä FIN-40351 Jyväskylä Finland +358 414740463 (mobile) +358 (0)14 260 4183 (office)

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Heteratom problems, message 1
by John Penniston 09 Nov '02

09 Nov '02

I've been trying for days to make a proper model of my large (1058 residue) membrane protein, PMCA. It needs to contain a calcium ion, but I can't get modeller to put it in. I'm sorry the attached files are so big, but it's a big molecule. I'm sending this as 2 messages, zipped up using Winzip; If I try to put it in a single message, it bounces, and I think all of these files are needed to diagnose the problem. I'm trying to model PMCA based on the only known homolog 1EUL. 1EUL contains 2 calcium ions, and I expect the PMCA version to contain only one of them, as indicated in the alignment file. No matter what I try, the PMCA file produced has the calcium removed. The file I have renamed as PMCA E1.pdb is the final file produced in the attempt enclosed here and described in the log file. I did this one using an MS-DOS box under Windows 98, but the same kinds of errors occur in Windows 2000. Thanks for your attention. John Penniston -- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA

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Heteroatom problem, message 2
by John Penniston 09 Nov '02

09 Nov '02

I've been trying for days to make a proper model of my large (1058 residue) membrane protein, PMCA. It needs to contain a calcium ion, but I can't get modeller to put it in. I'm sorry the attached files are so big, but it's a big molecule. I'm sending this as 2 messages, zipped up using Winzip; If I try to put it in a single message, it bounces, and I think all of these files are needed to diagnose the problem. I'm trying to model PMCA based on the only known homolog 1EUL. 1EUL contains 2 calcium ions, and I expect the PMCA version to contain only one of them, as indicated in the alignment file. No matter what I try, the PMCA file produced has the calcium removed. The file I have renamed as PMCA E1.pdb is the final file produced in the attempt enclosed here and described in the log file. I did this one using an MS-DOS box under Windows 98, but the same kinds of errors occur in Windows 2000. Thanks for your attention. John Penniston -- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA

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Loop Modeling
by Alex Brown 07 Nov '02

07 Nov '02

Dear Modellers, I have been running through the examples in the Fiser and Sali paper concerning the modeling of the loop in cpCN-V (circularly permuted cyanovirin). I used the given scripts, modifying it to allow the modeling of different linker lengths, from 6 to 12 residues, as suggested in the paper. 200 final models of each linker were obtained, the model with the lowest energy score (objective function) being selected in each case. This gave the following table of results: Length (aa) Residues Objective Function Model # File Name 6 49-54 21.6408 119 cpCN-V.BL06 7 48-54 12.1955 49 cpCN-V.BL07 7 49-55 33.0729 118 cpCN-V.BL07a 8 47-54 7.5401 153 cpCN-V.BL08 8 49-56 35.8842 152 cpCN-V.BL08a 8 48-55 31.0163 117 cpCN-V.BL08b 9 46-54 12.1449 95 cpCN-V.BL09 9 49-57 24.4132 39 cpCN-V.BL09a 9 47-55 29.1883 145 cpCN-V.BL09b 9 48-56 27.4328 115 cpCN-V.BL09c 10 46-55 28.5179 184 cpCN-V.BL10 10 47-56 29.004 199 cpCN-V.BL10a 10 48-57 31.8589 25 cpCN-V.BL10b 11 46-56 18.1581 109 cpCN-V.BL11 11 47-57 22.4939 189 cpCN-V.BL11a 12 46-57 27.0164 198 cpCN-V.BL12 My question is, can I take the 'best' loop model as being that with the lowest objective function (i.e. model cpCN-V.BL08, objective function 7.5401). I did wonder how my results compared with those obtained by Fiser and Sali, but I have been unable to find this. Cheers, Alex Brown PS. I'm running Modeller v6.2 on Mac OS X (Darwin). Each modeling run (200 loop models) took 6-10 hours !!!!

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Re: problems
by Bozidar Yerkovich 01 Nov '02

01 Nov '02

Hi, Change: SET MD_LEVEL = 'refine1' To: SET MD_LEVEL = 'refine_1' Best, Bozidar > I wanted to use modeller6v2 with these attached files but I couldn't find > where is the problem. Would you help me please. I tested Modeller with the > file in the diretory examples/ and it worked well. So I couldn't understand... INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET MD_LEVEL = 'refine1' SET STARTING_MODEL=1 SET ENDING_MODEL=10 SET DEVIATION = 4.0 SET KNOWNS='1ORD' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET ALIGNMENT_FORMAT = 'PIR' SET SEQUENCE='gadmid' SET ALNFILE='AligntPubli1.ali' CALL ROUTINE='model' > Thank you very much > > Violaine Moreau > Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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