May 2005 - modeller_usage

dihedral restraints
by Judy Barnett-Norris 30 May '05

30 May '05

Hello, I have been reading about the restraints and have a question. I am modeling a GPCR using rhodopsin's crystal structure as my template. I want to model one area of a helix using some backbone dihedral values different from rhodopsin (10 actual dihedrals). Do I use the special.restraints script and list my specific dihedrals or do I need to do something similar to the cis proline example where I would unpick and then add each restraint?? If you could just point me in the direction.... Thanks, Judy

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problem with modeller
by Maria.Teresa.Azzollini＠roma1.infn.it 30 May '05

30 May '05

Hi! I couldn't find this problem already posted: until yesterday modeller8v0 was working perfectly without any problem. Today I tried to create models using the same input files of yesterday and it doesn't give me results anymore. In the .log file it is written: Kind, OS, HostName, Kernel, Processor: 4, Linux job.saclay.cea.fr 2.6.9-1.667 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): 2005/05/30 15:54:25.936 runcmd______> alignment.append(align_codes=['1E6I', '1EQF', 'SNF2'], atom_files=[], file='buonino3.ali', add_sequence=True, (def)alignment_format='PIR', (def)remove_gaps=True, (def)close_file=True, (def)rewind_file=False) openf___224_> Open buonino3.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 1919549 1874.560 1.831 Dynamically allocated memory at amaxalignment [B,kB,MB]: 1921249 1876.220 1.832 Dynamically allocated memory at amaxalignment [B,kB,MB]: 1924649 1879.540 1.835 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2134891 2084.854 2.036 Read the alignment from file : buonino3.ali Total number of alignment positions: 119 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1E6I 110 1 1E6I 2 1EQF 110 1 1EQF 3 SNF2 110 1 SNF2 runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1E6I rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 330: A To find out more, switch on maximal output by 'log.verbose()' Dynamically allocated memory at amaxstructure [B,kB,MB]: 2135661 2085.606 2.037 openf5__224_> Open 11 OLD SEQUENTIAL 1E6I rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 330: A To find out more, switch on maximal output by 'log.verbose()' rdabrk__288W> Protein not accepted: 1 69,1 Bot Everything is the same: the alignment file, the template files are in the right directory. What could be the problem? I post also the alignment file and the input file: >P1;1E6I structureX:1E6I:330 :A:439 :A:::-1.00:-1.00 G--PHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKM-EDFIYDARLVFN NCRMYNG-ENTSYYKYANRLEKFFNNKVKEIP---E--YSHLID* >P1;1EQF structureX:1EQF:1382 :A:1491 :A:::-1.00:-1.00 MVT-LSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLY-PSREEFREHLELIVK NSATYNGPK-HSLTQISQSMLDLCDEKLKEKEDKLARL------* >P1;SNF2 structureX:SNF2:FIRST: :110 : :::-1.00:-1.00 ALDLYHFALNYENEAGRKLSDI--FLSKPSKALYPDYYMIIKYPVAFDNINTHIETLAY-NSLKETLQDFHLIFS NARIYNT-EGSVVYEDSLELEKVVTKKYCEIMGDNSQL-----D* ~ from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:./atom_files' a = automodel(env, alnfile = 'buonino3.ali', # alignment filename knowns = ('1E6I','1EQF'), sequence = 'SNF2') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model a.make() # do the actual homology modelling ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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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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