- modeller_usage - salilab.org

heme moiety of CYP450
by O'MAHONY, BRIAN 30 May '05

30 May '05

Hi all, I am modelling a cytochrome and want to make a model with the heme heteroatoms in the model. I have been superimposing a heme from one of the templates but this doesn't work when I go to relax my model. I also see that Modeller can model heteroatoms but I cannot find a script that works, ie. when I put the command HETATM_IO = 1 or even on or zero (can't remember off hand which command is correct. Modeller goes ahead and builds models but without the heme moiety. Does anyone have a script that works for Modeller v6.3. I've already tried the one in the manual. Brian O'Mahony Institut Municipal de Investigació Mèdica (IMIM) Pharmacology Research Unit Dr. Aiguader, 80 E-08003 Barcelona, Spain Tel: +34 - 93 225 25 97 E-mail: mailto:bomahony@imim.es Web: http//www.imim.es

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signif_cutoff
by Jean-Marc Vuissoz 27 May '05

27 May '05

hello, I am searching more info about sequence_db.search and it's parameter particularly signi_cutoff ; fast_search_cutoff ; and gap_penalties_1d what are "good" value best thanks jm

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modeller 8v0 on Centos4 (aka RHEL 4)
by Ezequiel H Panepucci 27 May '05

27 May '05

Hello, I've recently installed Modeller 8v0 on Linux (Centos 4 which is derived from Redhat Enterprise Linux 4) and it is giving me a hard time. Below is what happens running examples/automodel/model-default.py. It happens using both the *tar.gz or *rpm installs. It gives similiar problems on Redhat 9 as well. Thanks in advance! Zac $ mod8v0 model-default.py forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libc.so.6 009F6B3D Unknown Unknown Unknown mod8v0_i386-intel 0812A85D Unknown Unknown Unknown mod8v0_i386-intel 08106CC8 Unknown Unknown Unknown mod8v0_i386-intel 082A6647 Unknown Unknown Unknown mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown mod8v0_i386-intel 082ED02E Unknown Unknown Unknown mod8v0_i386-intel 08258A54 Unknown Unknown Unknown mod8v0_i386-intel 082A5252 Unknown Unknown Unknown mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown mod8v0_i386-intel 082A7628 Unknown Unknown Unknown mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown mod8v0_i386-intel 082A7FB6 Unknown Unknown Unknown mod8v0_i386-intel 082C9800 Unknown Unknown Unknown mod8v0_i386-intel 082CA0E6 Unknown Unknown Unknown mod8v0_i386-intel 082CB1EB Unknown Unknown Unknown mod8v0_i386-intel 080D40A7 Unknown Unknown Unknown mod8v0_i386-intel 08076E94 Unknown Unknown Unknown mod8v0_i386-intel 08076B2D Unknown Unknown Unknown libc.so.6 009A1E33 Unknown Unknown Unknown mod8v0_i386-intel 080769C1 Unknown Unknown Unknown

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model8v0
by bu weiming 24 May '05

24 May '05

Hi, All I'm tring to run Modeller v8 on sgi Octane(irix6.5). There was warning: ulimit exceed allowable limits. After I unlimited the stacksize, I still can't run Modeller. after the command "mod8vo", the message " usage modv80 script" appreared. BTW, modeller 6.2 is working fine on this computer, but I want to use the current version. Any help would be highly appreciated. regards Wei ming __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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multiple templates
by Swagatam Ray 21 May '05

21 May '05

Hi, I want model a protein with 3 domains similar to 3 different proteins in PDB hit. can I use them all simaultaneuosly as a template. I don't want to use chimera strategy as it may give wrong information regarding the overall curvature at junction points (if I understood correctly!). Thanks, Swagatam Ray

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Problem about tutorial (Iterative Example)
by Jianying (Julia) Ding 20 May '05

20 May '05

Dear modller users, I have a question about the tutorial, specifically it is the iterative example. I found after the alignment, model can NOT be generated, I ran it for my own problem and the example downloaded from the website, both of them are not working. The log file is pasted below. Obviously it indicated the PDB file is not found. That's very odd. Does anybody know where is the problem? I appreciate your help. Julia 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 magnesium 2.4.21-27.EL i686 Date and time of compilation : 04/15/2005 15:55:19 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/05/19 12:48:32.321 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 4dfr

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(no subject)
by Michael Grabe 20 May '05

20 May '05

dear modellers, has anyone written their own absolute space restraints for the x,y or z cooridinates and gotten it to work? if so, i would love sample scripts with the restraints file and all the accouterments. thanks so much, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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Spatial restraints as "flat bottom" potential
by Esben Jannik Bjerrum 19 May '05

19 May '05

I'm trying to model a flexible protein where two highly rigid domains move in respect to each other, and would like to model some of the states between the two extremes in the templates. When I model with the open and closed form of the protein as templates, I only get open and closed forms af the target. As I initially understood the spatial restraints, they are an average of the restraints extracted from the templates. But it seems to me now, that when theres a spatial restraint of f.ex 6� from one template and 8� from the other, modeller tries to match either 6� or 8� in the target, where 7� is not OK. Please correct me if I misunderstood. Is it possible to change this behaivor to a flat bottom potential? To take the former example: So that any distance in the range 6-8� is equal, and the potiential then rising outside that? Due to glibc compat. errors i've used mod6v2 and not the newest 8v0. Best Regards Esben Jannik Bjerrum __________________________________ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail

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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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