- modeller_usage - salilab.org

profile files
by Jason M Walraven 01 Sep '05

01 Sep '05

How can I view a graph of the evaluate_model.py profile files? An example graph is given in the tutorial, but no info on how to view it in graphical form. Do I manually transfer the DOPE score values from the file to a graphing program, or is there an easier way? Thanks!

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crsplin_223E> Internal error: array too small: MAXSPL current maximum, current need: 400 420.
by Guido Leoni 26 Aug '05

26 Aug '05

Hi I'm dealing with a little big problem (for me). I need to model a dymer protein. My structures are 952, 958, 898 residues long and my sequence is formed by 990aa. When Modller run send my this error message: crsplin_223E> Internal error: array too small: MAXSPL current maximum, current need: 400 420. Someone can help my? Thank you very much

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template pdb file has no header
by Akansha Saxena 26 Aug '05

26 Aug '05

Hello Modeller Caretaker I want to use automodel class of modeller to develop a model of an unknown sequence based on one template. I have a pdb file for the template but this pdb file does not have its convenational header information, remarks, etc. I guess modeller is not able to recognise my file as a valid pdb file. Kindly tell me how to use this pdb file as a template file. Akansha __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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[modeller_usage]
by sankari thirumal 26 Aug '05

26 Aug '05

Hi all I'm new to this area. Just installed modeller in the windows XP and run the test model. Now i have to model a protein with 500 amino acid residues, for which there are no pdb matches in the pdb database. So i have gone for pfam domain search. I found that a domain with 500 residues and from 30-494 is aligning with my sequence with a e value of 3e-11. Can i take this portion as a template for modelling? and what should i do for the remaining amino acids (1.e) 1-29 and 494-500.? should i follow the steps involved in advance modelling? please do explain me the steps involved with regards sankari __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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modeller usage
by Guido Leoni 09 Aug '05

09 Aug '05

*Hi, I'm a new modeller use and* * I am trying to use the modeller8v1version on my windows machine to model my protein. but it keeps giving me this following error. Though all the script file, alignment files and pdb files are in the same directory as specified in the script file.* TypeError: 'tuple' object has only read-only attributes <assign to .starting_model>. *My script is*: # Homology modelling by the automodel class from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = 'C:\Documents and Settings\Zio Charlie\Desktop\PROVE MODELLER2', a = automodel(env, alnfile = 'ali4.aln', # alignment filename knowns = ('1EW2_A', '1K7H_A', '1ED9_A'), sequence = 'gi|14521248|ref|NP_126723.1|'), a.starting_model = 1 a.ending_model = 1 a.make() *and my alignment file is:* >P1;gi|14521248|ref|NP_126723.1| sequence:gi|14521248|ref|NP_126723.1|:1 : --MMKMKLARFLLIFIIFSSMFP----------FANASPSGVRNVIILIG DGMGFSQLQLTKLVYGHLN-----------MEDFPYTGIELTDSLSGEVT DSAAAGTAIATGVKTYNRMISTTNVTGKLVNLTT---------LLEIAQM LGKATGLVTTTRITHATPAVFASHVPDR-------------------DME EEIARQLILHNVTVLMGGGREKFS-----------EEVLKLAEDYGYSIV YTREDLEKVKDG-------------------------KVLGLFAEGHLPY VLDR-SEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVAS IVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDI DSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNST NKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHV DTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLL GDLVDTELENIADMDNNGIIDLLDVMAILQASS* >P1;1ED9_A structure:pdb_file:1ED9:1 : TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIG DGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVT DSAASATAWSTGVKTYNGALGVDIHEKDHPT------------ILEMAKA AGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGK GSITEQLLNARADVTLGGGAKTFAET-ATAGEWQGKTLREQAQARGYQLV SDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCT PNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCG QIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA-----------HASQI VAPDTKAP---GLTQALNTKDGAVMVMSYGNSE----------------- --------------------EDSQEHTGSQLRIAAYGPHAANVVGLTDQT DLFYTMKAALGLK------------------------------------- ---------------------------------* >P1;1EW2_A structure:pdb_file:1EW2:1 : --IIPVEEENPDFWNREAAEALG-------AAKKLQPAQTAAKNLIIFLG DGMGVSTVTAARILKGQKKDKLG-PEIPLAMDRFPYVALSKTYNVDKHVP DSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVIS--VMNRAKK AGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQ-EGCQDIA TQLISN---MDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLV QEWLAKRQ--------GARYVWNRTELMQASLDPSVTHLMGLFEPGDMKY EIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYR ALTETIMFDDAIERAGQLTSEE-DTLSLVTADHS-----------HVFSF GGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESE SGSPE-------YRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQT FIAHVMAFAACLEP-YTACDLAPPAGTTDAAHPGRSVVP----ALLPLLA GTLLLLETATAP---------------------* >P1;1K7H_A structure:pdb_file:1K7H:1 : -------EEDKAYWNKDAQDALD-------KQLGIKLREKQAKNVIFFLG DGMSLSTVTAARIYKGGLTGKFE-REK-ISWEEFDFAALSKTYNTDKQVT DSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQE AGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDREDPEICDDIA EQLVFREPGKNFKVIMGGGRRGFF----PEEALDIEDGIPGEREDGKHLI TDWLDDKASQGA----TASYVWNRDDLLAVDIAN-TDYLMGLFSYTHLDT VLTRDAEMDPTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQ SLAETLDMEEAVSMALSMTDPE-ETIILVTADHG-----------HTLTI TGYADRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEED LKDIN-------FRYASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEEN YIPHALAYAACVGTGRTFCD------------------------------ ---------------------------------* Can some one suggest a solution? Thanks Guido

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Hydrophobic restraints question
by qiuyan_wang＠email.jlu.edu.cn 08 Aug '05

08 Aug '05

Dear my modellers: I am modeling a chimeric protein from two different proteins, which have known structures. There is no overlap between them,so i oriented two domains before the modeling. But i got an unreasonable model in which one domain so called 'lid' was just beside the other catalytic domain,even under some distance restraints to some reference residues i used. It is believed that hydrophobic interaction drives two domains forming a closed conformation. So,should i use something like hydrophobic restraints to the modeling, and how to do this? Thanking you in advance.

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Error: Unable to open alignment file
by Amin Momin 08 Aug '05

08 Aug '05

Hi, I am trying to use modeller8v1 on my windows machine to model my protein. but it keeps giving me this following error. Though all the script file, alignment files and pdb files are in the same directory as specified in the script file. Can some one suggest a solution. Thanks Amin openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1FC4', 'SPT1ham'], atom_files=[], file='alignment.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___670E> Cannot open file alignment.ali: No such file or directory

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Modeller 8 forrtl severe 157
by Rodrigo Reston 04 Aug '05

04 Aug '05

Hi! I was about to start using Modeller with the model-default.py script and I got my first error message: forrtl: severe (157): program exception - access violation. I couldn't find any reference to it on Google. Could you help me? I'm running Modeller 8 on Windows 2000 sp4 Toshiba Satellite A10 S1001 Intel Celeron 2.5GHz. Thanks. Rodrigo

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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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