May 2005 - modeller_usage

modv8.0 on amd64
by Kim Branson 18 May '05

18 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi i'm trying to get the generic unix build of modeller to run on a amd64 bix running fedora core 3. I've had a look at the python paths, and played with a few variables. It would seem the python interpreter cannot find the site packages, but imports the modeller addons fine. Does anyone have a tip on how to get the embedded python to find the site packages? export PYTHONPATH=/usr/lib64/python2.3/ #export PYTHONHOME=/usr/local/modeller8v0/bin/lib/python2.3 export PYTHONHOME=/usr/lib64/python2.3/ [kbranson@culpeper ~]$ mod8v0 - MODELLER 8v0, Apr 15, 2005 03:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2005 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, M. Topf, 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 culpeper.parkville.hsn.csiro.au 2.6.10-1.766_FC3smp x86_64 Date and time of compilation : 04/15/2005 15:36:51 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/05/14 11:21:41.002 'import site' failed; use -v for traceback >>> dir() ['ModellerError', '__builtins__', '__doc__', '__name__', 'alignment', 'density', 'energy_data', 'environ', 'group_restraints', 'info', 'io_data', 'libraries', 'log', 'model', 'modfile', 'profile', 'sequence_db', 'topology', 'util'] Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson(a)svi.edu.au kim.branson(a)gmail.com www.svi.edu.au -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) iD8DBQFChVOI3QNu8KNs0LgRAqpeAJ9k0YGk86O16X1E0+yyHFS40qsVOQCgzpdk e6+2s8zwGNWoAlpl5P2CFWs= =f5X8 -----END PGP SIGNATURE-----

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absolute position restraints
by "Frank Böckler" 17 May '05

17 May '05

Dear all, I'm trying to keep some part (ligand) fixed in space using the restraint features 9, 10 and 11 and the restraint type 34. Unfortunately, I was not quite successful with this approach (outlined below). Can anybody give me an advice, how to proceed correctly (correct syntax for the restraints, other approach giving the same result, ...)? Any help is highly appreciated! Thanks in advance, Frank My approach was: # generating a restraint file from the .ini file of a corresponding run, which included the ligand (atom-ids: 1936-1958) using an awk script: .ini-file: HETATM 1936 C5 LAE 257 46.483 11.136 15.931 1.00 -0.04 4SG1940 HETATM 1937 C4 LAE 257 45.927 12.329 16.596 1.00 0.07 4SG1941 [...] HETATM 1958 C16 LAE 257 42.378 10.076 17.821 1.00 -0.02 4SG1962 END .rsr-file: MODELLER5 VERSION: MODELLER FORMAT R 3 1 9 34 1 2 0 1936 46.483 0.0 R 3 1 10 34 1 2 0 1936 11.136 0.0 R 3 1 11 34 1 2 0 1936 15.931 0.0 R 3 1 9 34 1 2 0 1937 45.927 0.0 R 3 1 10 34 1 2 0 1937 12.329 0.0 R 3 1 11 34 1 2 0 1937 16.596 0.0 [...] R 3 1 9 34 1 2 0 1958 42.378 0.0 R 3 1 10 34 1 2 0 1958 10.076 0.0 R 3 1 11 34 1 2 0 1958 17.821 0.0 My idea was to constrain the x, y or z coordinate (feature 9, 10, 11) of the ligand with a harmonic potential (3) written into restraint type 34 and applied on 1 atom (using 2 parameters: the coordinate and the standard deviation). I've used both 0.0 and higher values as standard deviations to fix the atom position absolutely or to allow some movement, however both was unsuccessful. Perhaps the whole syntax is false??? However, modeller7v7 does not complain about the restraints (as can be seen from the .log file), which I read in as part of my rewritten 'special_restraints' section: .top-file: subroutine routine = 'special_restraints' [...] read_restraints file = '/home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr', add_restraints = on [...] return end_subroutine .log-file: [...] make_re_422_> Number of previous, current restraints : 20593 20593 make_re_423_> Number of previous, current selected restraints: 20327 20327 [...] TOP_________> 218 750 CALL ROUTINE = 'special_restraints' [...] TOP_________> 223 761 READ_RESTRAINTS FILE = '/home/literatur/boeckler/D4proj/t; op/LIG_posconst_new2.rsr', ADD_RESTRAINTS = ON openf5__224_> Open 11 OLD SEQUENTIAL /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr openf5__224_> Open 11 OLD SEQUENTIAL /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr rdcsr2__307_> Number of restraints read : 69 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 18611512 18175.305 17.749 openf5__224_> Open 11 OLD SEQUENTIAL /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr openf5__224_> Open 11 OLD SEQUENTIAL /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr rdcsr2__307_> Number of restraints read : 69 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 20662 20396 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 [...] Thus, it seems that the restraints have been read in successfully and no errors were reported. However, having a look at the output file shows that the ligand has been "exploding", spreading its atoms all in space. .pdb-file: HETATM 1936 C5 LAE 257 127.363 17.224 57.224 1.00 57.83 4SG1940 HETATM 1937 C4 LAE 257 50.824 -79.520 -76.644 1.00 57.83 4SG1941 [...] HETATM 1958 C16 LAE 257 66.463 23.642 160.673 1.00 57.83 4SG1962 END -- ------------------------------------------------------------------ Dr. Frank Böckler Dept. of Medicinal Chemistry Emil-Fischer-Center Friedrich-Alexander University Erlangen-Nürnberg Germany ------------------------------------------------------------------ +++ Lassen Sie Ihren Gedanken freien Lauf... z.B. per FreeSMS +++ GMX bietet bis zu 100 FreeSMS/Monat: http://www.gmx.net/de/go/mail

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segmentation fault
by mdatt＠imtech.res.in 17 May '05

17 May '05

hi when i corrected my alignment file as suggested, instead of getting bus error, now i`m getting segmentation fault. it seems there is still some problem with the alignment file. i would deeply appreciate if you could pin point the error. another query that i`ve is that whether the gaps in sequence of the structure make the sequece non contigous. if that is so then how to take cate of it. thanks for any help Manish Datt

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forcing alignment of particular residues
by gerald.quon＠utoronto.ca 17 May '05

17 May '05

Hi, I'm wondering how to force the align2d procedure to align the sequences to the structures, under the constraint that a particular residue be aligned in all sequences. i.e. is there a better way than to split the alignment into two alignment procedures?

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bus error
by mdatt＠imtech.res.in 12 May '05

12 May '05

hi all on doing comparative modelling using modeller v8 i got bus error. here i'm attaching my input files thanks for any help Manish Datt

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(no subject)
by Manish Datt 11 May '05

11 May '05

hi all i`ve recently installed modeller v8 on sgi irix machine. when in tried to perform comparative modeling, using the script given in examples, i got bus error. also there was warning: ulimit exceed allowable limits. on checking i discovered that ulimit has been set to unlimited. any help would be highly appreciated. regards, Mansih Datt Research Fellow Bioinformatics Centre IMTECH Chandigarh, India.

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tetramers in symmetry
by hchoe 09 May '05

09 May '05

Dear Modellers, I have used the following subroutine to define tetramers in symmetry. Please tell me how to do it in MODELLER8v0. SUBROUTINE ROUTINE = 'defsym' SET RES_TYPES = 'ALL', ATOM_TYPES = 'MNCH', SELECTION_STATUS = 'INITIALIZE', SELECTION_SEARCH = 'SEGMENT', SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '37:' '322:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '323:' '608:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '323:' '608:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '609:' '894:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '609:' '894:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '895:' '1180:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '895:' '1180:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '37:' '322:' DEFINE_SYMMETRY ADD_SYMMETRY = on off RETURN END_SUBROUTINE Thanks in advance. Cheers, Han

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heteroatom
by arul prakasam 08 May '05

08 May '05

dear sir iam modeling a model which has heteroatom FE2 at its active site my template and target has FE2 what should i do to model this ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony

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