- modeller_usage - salilab.org

What I'm doing wrong?
by Antonio Arroyo Luque 08 Sep '05

08 Sep '05

Hello Everyone, I'm trying to follow the tutorial. And this is what I get. Any help? Thank you Antonio Arroyo Note: Translation at the end is added by myself. *************************************************************************** Type 'mod8v1 model-default.py' to run Modeller on the script 'model-default.py'. F:\Archivos de programa\Modeller8v1>mod8v1 model-default.py FATAL ERROR: Cannot open file model-default.py: No such file or directory F:\Archivos de programa\Modeller8v1>c: C:\>cd basic-example C:\basic-example>dir El volumen de la unidad C es Esclavo El número de serie del volumen es: 9013-03E9 Directorio de C:\basic-example 08/09/2005 10:37 <DIR> . 08/09/2005 10:37 <DIR> .. 10/06/2005 17:03 246.159 1b8p.pdb 10/06/2005 17:03 453.033 1bdm.pdb 10/06/2005 17:03 142.581 1bdmA.profile 10/06/2005 17:03 3.198 1bdmA_dope.dat 10/06/2005 17:03 277.749 1civ.pdb 10/06/2005 17:03 1.606.878 1smk.pdb 10/06/2005 17:03 500.477 5mdh.pdb 10/06/2005 17:03 970.763 7mdh.pdb 10/06/2005 17:03 2.940 align2d.log 10/06/2005 17:03 349 align2d.py 10/06/2005 17:03 11.927 build_profile.ali 10/06/2005 17:03 16.593 build_profile.log 10/06/2005 17:03 13.540 build_profile.prf 10/06/2005 17:03 1.252 build_profile.py 10/06/2005 17:03 122.300 compare.log 10/06/2005 17:03 236 compare.py 10/06/2005 17:03 17.178 dope_evaluation.pdf 10/06/2005 17:03 180.013 evaluate_model.log 28/06/2005 10:38 890 evaluate_model.py 10/06/2005 17:03 167.409 evaluate_template.log 28/06/2005 10:37 860 evaluate_template.py 10/06/2005 17:03 215 family.mat 06/09/2005 10:08 1.483 model-default.log 06/09/2005 11:00 68.299 model-single.log 10/06/2005 17:03 193 model-single.py 10/06/2005 17:03 5.063.163 pdb_95.pir 10/06/2005 17:03 819 TvLDH-1bdmA.ali 10/06/2005 17:03 1.538 TvLDH-1bdmA.pap 10/06/2005 17:03 383 TvLDH.ali 06/09/2005 10:47 213.789 TvLDH.B99990001.pdb 06/09/2005 10:51 213.789 TvLDH.B99990002.pdb 06/09/2005 10:54 213.789 TvLDH.B99990003.pdb 06/09/2005 10:57 213.789 TvLDH.B99990004.pdb 06/09/2005 11:00 213.789 TvLDH.B99990005.pdb 06/09/2005 10:46 24.990 TvLDH.D00000001 06/09/2005 10:50 25.305 TvLDH.D00000002 06/09/2005 10:53 25.620 TvLDH.D00000003 06/09/2005 10:56 25.200 TvLDH.D00000004 06/09/2005 10:59 25.410 TvLDH.D00000005 06/09/2005 10:44 213.733 TvLDH.ini 10/06/2005 17:03 150.163 TvLDH.profile 06/09/2005 10:44 2.188.086 TvLDH.rsr 06/09/2005 10:57 3.121 TvLDH.sch 06/09/2005 10:47 150.529 TvLDH.V99990001 06/09/2005 10:51 150.529 TvLDH.V99990002 06/09/2005 10:54 150.529 TvLDH.V99990003 06/09/2005 10:57 150.529 TvLDH.V99990004 06/09/2005 11:00 150.529 TvLDH.V99990005 10/06/2005 17:03 3.351 TvLDH_dope.dat 49 archivos 14.378.987 bytes 2 dirs 53.856.186.368 bytes libres C:\basic-example>>P1;TvLDH "TvLDH" no se reconoce como un comando interno o externo, [Translation: "TvLDH" is not recognized as either an internal or external command, programa o archivo por lotes ejecutable. program or a batch-script file] Sorry if not well translated C:\basic-example> *******************************************************************

2 1

Nucleic acid-protein complexe
by Charlotte Habegger-Polomat 07 Sep '05

07 Sep '05

Hello! This is a question I posted a while back with no answer. I'm trying again in hopes that this is the right spot and that someone can help me out with this! I have successfully modelled a protein using Modeller with three template structures from the PDB. I now would like to add on a tRNA which is present in other homologous structures in the PDB. Must I redefine nucleic acids in the Modeller files or should Modeller be able to recognize common nucleic acid "residues"? Any suggestions as to how to obtain a quick first model of the complex will be greatly appreciated! Thank you! -Charlotte Habegger-Polomat

1 0

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

3 2

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

2 1

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!

1 0

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

2 1

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

2 1

[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

1 0

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

1 0

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.

2 1