- modeller_usage - salilab.org

loop modelling
by Judy Barnett-Norris 04 Aug '05

04 Aug '05

Hello, I just wanted to ask a few questions...I am modelling loops on a GPCR. My current script follows my questions. 1. Will I get better sampling by running 20 different runs (with different random number seeds) that create 25 models each thus a total of 500 models? 2. Would setting dynamic_coulomb = True and a relative _dielectric = 80 be the best way to simulate an aqueous environment for the loops? 3. Is it possible to run the loop optimization with explicit hydrogens? I guess my env.io.hydrogen = True does not actually set up the calculation to do explicit hydrogens but only tells Modeller to read the hydrogens from my pdb file. 4. For the refinement level, I am using md_level = refine.very_slow for what size system is the refine.slow_large used? 5. Would I get better sampling by setting repeat.optimization greater than 1? Thank you in advance. Judy Norris ========================================================================== #Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() env = environ(rand_seed=-32601) env.io.atom_files_directory = './:../atom_files' env.edat.dynamic_coulomb = True env.edat.relative_dielectric = 80 env.io.hydrogen = True class myloop(loopmodel): def select_loop_atoms(self): stat = 'INITIALIZE' for segs in (('1:', '15:'), ('49:', '54:'), ('84:', '89:'),('124:','133:'), ('226:','233:')): self.pick_atoms(selection_segment=segs, selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status=stat) stat = 'ADD' m = myloop(env, inimodel = 'protein_lp01.B99990001.pdb', # alignment filename sequence = 'protein_01') # code of the target m.loop.starting_model= 1 # index of the first model m.loop.ending_model = 25 # index of the last model # (determines how many models to calculate) m.loop.md_level = refine.very_slow # No refinement of model m.make() # do homology modelling =====================================================================

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modelling multiple loops
by David L. Bostick 27 Jul '05

27 Jul '05

Dear modellers, I have searched the archives of the discussion forum for this and found a few questions, but no answers. I wish to impart the template structure to a sequence exactly, and select only the loops for refinement. I am using modeller 7v7, and have not switched to 8 yet. I would be interested in ways to do this for both versions, but most interested in 7v7. Currently, I use a snippet of top script taken from one of the examples that looks like this: SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='100:' '105:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize' RETURN END_SUBROUTINE but I have no idea how to extend this to do multiple loop modelling all at the same time... i.e. segment 100-105, 158-164, 200-206, etc... all at once. I've tried lots of things, but I have not been able to figure out the syntax of top too well. I saw an email in the archive by Obdulia Rabal, who used something like SUBROUTINE ROUTINE = 'select_loop_atoms' READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE, ADD_SEQUENCE = off SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_MODE = 'ATOM' SET SELECTION_SEARCH = 'SEGMENT' SET SELECTION_FROM = 'ALL' SET GAP_EXTENSION = 2 2 # gaps are extended for two residues in both # directions to get loops (insertions & deletions) PICK_ATOMS SELECTION_SEGMENT = 'LOOPS' RETURN END_SUBROUTINE but he complained that the program still selected all the atoms for refinement, instead of only the loop portions. I've finally resorted to modelling every single loop separately, but this is no fun at all, and is time consuming. Can someone help please? Thanks, David -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= David Bostick Office: 262 Venable Hall Dept. of Physics and Astronomy Phone: (919)962-0165 Program in Molecular and Cellular Biophysics UNC-Chapel Hill CB #3255 Phillips Hall dbostick(a)physics.unc.edu Chapel Hill, NC 27599 http://www.unc.edu/~dbostick =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

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restraint violations files
by Maria Turano 25 Jul '05

25 Jul '05

What is the physical meaning of the field 3 (Stereochemical cosine torsion poten) and 4 (Stereochemical improper torsion pot) in the output file "nameprotein.V99990001"? Thank you for any suggestions. Maria Turano

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Restraining structure to Alpha
by John Penniston 20 Jul '05

20 Jul '05

I'm making a model which is supposed to contain an alpha helix in residues 26-46. I can do this with a top command file, by modifying the special_restraints subroutine in __special.top: SUBROUTINE ROUTINE = 'special_restraints' #This one is to adjust helices in fxyd proteins # SET ADD_RESTRAINTS = on # MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '14' '17' RETURN END_SUBROUTINE This works with the following alignment file, and gives me the uninterrupted helix I want. >P1;gamma structureX:gamma:FIRST:@:LAST : :undefined:undefined:-1.00:-1.00 MTGLSMDGGGSPKGDVDPFYYDYETVRNGGL------IFAGLAFIVGLLILLSRRFRCGGNKKRRQINEDEP* >P1;gamma1 structureX:gamma1:FIRST:@:LAST : :undefined:undefined:-1.00:-1.00 MTGLSMDGGGSPKGDVDPFYYDYET------VRNGGLIFAGLAFIVGLLILLSRRFRCGGNKKRRQINEDEP* When I use the same alignment file with a python routine copied from the FAQ, it runs fine but it doesn't apply the restraint! I'd like to use the new python command system for this kind of restraint, because the restraints are directly in the command file and not off in __special.top, but I can't make it work. Here is the python file I used: # comparative modeling of gamma from modeller.automodel import * # Load the automodel class #This one is to set the entire TM to a helix in gamma class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='ALPHA',residue_ids=('26','46')) log.very_verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in env.io.hetatm = True a = automodel(env, alnfile = 'gamma.ali', # alignment filename knowns = 'gamma', # codes of the templates sequence = 'gamma1') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling Thanks for your attention. John Penniston

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Correction- Restraining structure to Alpha
by John Penniston 20 Jul '05

20 Jul '05

Sorry; the Subroutine I used did not have comment lines for the restraints :-[ SUBROUTINE ROUTINE = 'special_restraints' #This one is to adjust helices in fxyd proteins SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '14' '17' RETURN END_SUBROUTINE

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Re: Newbie question : restraining secondary structure
by Frederico Arnoldi 17 Jul '05

17 Jul '05

Hi Parantu, I'm not an expert with modeller, but your problem, I guess, is a python problem. Python works with indented code, and, at the begining, it is lacking in your script. I hope it could be usefull, Frederico G. C. Arnoldi UNESP - Rio Claro - SP - Brazil. Pay attetion on the "spaces" before the statements. Maybe the the following script should work. class mymodel(automodel): def special_restraints(self, aln): ## an indentation rsr = self.restraints ### another rsr.make(aln, restraint_type='STRAND', residue_ids=('416', '418')) env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile = 'ewq_msh23.ali', # alignment filename knowns = '1EWQ', # codes of the templates sequence = '1msh') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling Message: 4 Date: Sun, 17 Jul 2005 14:20:39 +0200 (CEST) From: Parantu Shah <shah(a)embl-heidelberg.de> Subject: [modeller_usage] Newbie question : restraining secondary structure To: modeller_usage(a)salilab.org Message-ID: <Pine.LNX.4.44.0507171409470.861-100000(a)jack.EMBL-Heidelberg.DE> Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, May be I am making a mistake in here but. When I try to use the script in example 12 in the FAQ about * Is it possible to restrain secondary structure in the target sequence? modeller 8v1 gives following error message and quits File "model-default.py", line 7 rsr = self.restraints: ^ IndentationError: expected an indented block Any help is wellcome best regards, Parantu ---------------------------------------------------- * Here is the script file from modeller.automodel import * # Load the automodel class class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND', residue_ids=('416', '418')) env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile = 'ewq_msh23.ali', # alignment filename knowns = '1EWQ', # codes of the templates sequence = '1msh') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling ------------------------------------------------------------------------- Parantu Shah Ph: 0 6221 387 456 (0) Graduate Student : 0 1797 731 953 (m) Bork Group Fax: +49 6221 387 517 European Molecular Biology Laboratory Heidelberg, Germany _________________________________________________________________ Chegou o que faltava: MSN Acesso Grátis. Instale Já! http://www.msn.com.br/discador

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Newbie question : restraining secondary structure
by Parantu Shah 17 Jul '05

17 Jul '05

Hi, May be I am making a mistake in here but. When I try to use the script in example 12 in the FAQ about * Is it possible to restrain secondary structure in the target sequence? modeller 8v1 gives following error message and quits File "model-default.py", line 7 rsr = self.restraints: ^ IndentationError: expected an indented block Any help is wellcome best regards, Parantu ---------------------------------------------------- * Here is the script file from modeller.automodel import * # Load the automodel class class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND', residue_ids=('416', '418')) env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile = 'ewq_msh23.ali', # alignment filename knowns = '1EWQ', # codes of the templates sequence = '1msh') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling ------------------------------------------------------------------------- Parantu Shah Ph: 0 6221 387 456 (0) Graduate Student : 0 1797 731 953 (m) Bork Group Fax: +49 6221 387 517 European Molecular Biology Laboratory Heidelberg, Germany www.bork.embl-heidelberg.de/~shah GCS/S d- s: a- c++++$ UL+++$ P++++$ E--- W++ N-- O++ !K W++ N-- o+ !K W !O M V PS+ PE++ Y+ PGP+ t+ !5 X+ R- tv++ b+++ DI+ !D G++ e+++(++++) h+ r y+ z?

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mod8v1: command not found
by Bo Yang 14 Jul '05

14 Jul '05

Hello, I have installed the Mod8v1 into the Mac and Window. It works fine with the Window, but has a problem with Mac. Here is How I did: ----- mriv209-01:Modeller/examples/automodel] bo% mod8v1 model-default.py tcsh: mod8v1: Command not found. ---- I installed the Modeller under 'users/bo/Application", I can see all the files there. I don't know why it does not work, although I am not in the 'adminstration'. The Mac is Mac OS X, Version 10.3.9 Thank you for any suggestions. Boy __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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allhydrogen model and nselat error
by Starr Hazard 14 Jul '05

14 Jul '05

Folks, I am experimenting with leaving crystal waters in my template structures. I am also trying the python scripting for the first time. I have been trying to get MODELLER8v1 to accept a single template. The template has hydrogens as do the waters. This works out to 6324 atoms. The rsr file has lots of entries for atom 6324. This suggests that counting atoms is not a problem. The execution stops with an csrng and a nselat error indicating that the atom index is out of bounds and out of range. The atom numbers are for 6320 an 6319. 6319 is an oxygen; 6320 one of its hydrogens. "csrrng__299E> Atom index is out of bounds: 6320 6319 nselat__596E> Atom index is out of range (iatm,natm): 6320 6319" Both 6319 and 6320 have lots of entries in the rsr file. 6320 appears to have many more entries than 6319. Here is the primative python script I am exploring. # Very fast homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' env.io.water= True a = allhmodel(env, alnfile='wwat.pir', # alignment filename knowns= ('PDB'), # codes of the templates sequence='G1', # code of the target # assess_methods=('assess.DOPE', 'assess.GA341') # request DOPE and GA341 model assessment ) a.very_fast() # prepare for extremely fast optimization a.starting_model = 1 a.ending_model = 5 a.final_malign3d = True a.make() # make the homology model What can do to troubleshoot this? Starr

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Modeller 8v1 on x86_64
by Jarrod Smith 13 Jul '05

13 Jul '05

With the generic UNIX install of Modeller 8v1 on x86_64 RHEL 3, the site packages cannot be found: 57 scylla:/sb/apps/modeller8v1/examples/all-steps% mod8v1 search.py 'import site' failed; use -v for traceback To work around this, I've added the following line to our mod8v1: if test "$ARCH" = "x86_64"; then export PYTHONPATH=/usr/lib64/python2.2; fi There may be other ways to fix it, but this worked for me. -- Jarrod A. Smith, Ph.D. Asst. Director, Center for Structural Biology Research Asst. Professor, Biochemistry Vanderbilt University

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