- modeller_usage - salilab.org

Tutorial for beginners?
by Antonio Arroyo Luque 06 Sep '05

06 Sep '05

Hello everyone, I try to lunch and run Modeller8v1 without any success. I use either the Windows or the Mac version of the program. The problem I have is that I don't know anything about Informatics but I want to learn. The tutorial of Modeller I've found assumes certain knowledge of Informatics. For instance, how do I launch Modeller? From the prompt of a OS terminal? How to say to the program where my files are located? I have this problem since version 6 of Modeller (more than 2 years ago) and since that I've been downloading new versions of the program but as I said without any success. Is there any basic, basic, basic (something like Modeller for Dummys - as I am) tutorial to start with? I will very appreciate your help. Also, any Spanish people working with Modeller? Thank you very much Antonio

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Internal error: array too small
by hchoe 01 Sep '05

01 Sep '05

Dear Modeller, I've got this error message. dihdisn_223E> Internal error: array too small: current maximum, current need: 100 101 What should be fixed? Thanks in advance.. Cheers, Han

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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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