- modeller_usage - salilab.org

Pick Restraints
by John Penniston 16 Jun '05

16 Jun '05

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problems with modeller
by limongelli＠unina.it 16 Jun '05

16 Jun '05

To whom it may concern, I'm a researcher of Naples University and I'm using modeller for my work. I've followed correctly the Basic tutorial with my enzyme in the place of lactate dehydrogenase. The program run but I got many warnings in the following .log files: 1) when I run "mod8v0 compare.py" I got this warning: fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA 2) when I run "mod8v0 align2d.py" I got these warnings: iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA 3) when I run "mod8v0 model-single.py" I got these warnings: fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 275 atom names : C +N atom indices : 2252 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 275 atom names : C CA +N O atom indices : 2252 2247 0 2253 fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA omgdel__425W> Unselected all O C +N +CA dihedrals: 282 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 21721 19723 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. Could someone please help me to find where I did wrong Thanks in advance Vittorio ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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array too small
by John Penniston 10 Jun '05

10 Jun '05

2 3

Modelling a nucleic acid ligand present in the PDB file
by Charlotte HABEGGER-POLOMAT 08 Jun '05

08 Jun '05

Hello! Having obtained a satisfactory 3D model of my protein using Modeller with structures known in the PDB for three homologs, I would like to add a nucleic acid ligand (a tRNA). None of the three PDB structures I used contained the nucleic acid, but I have other PDB files for one of the three homologs with the same nucleic acid. In the PDB files for the known protein/nucleic acid complex, the coordinates for the nucleic acid are not under HETATM residues but simply as ATOMS after the protein coordinates. What would be the simplest way to build a first quick model of my protein with the tRNA just to get an idea of the complex? Thanks for any suggestions! -Charlotte (I am originally subscribed under chpoloma(a)rsvs.ulaval.ca) _____________________________________________________________________________ Découvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vidéos ! Créez votre Yahoo! Mail sur http://fr.mail.yahoo.com

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Python command
by John Penniston 07 Jun '05

07 Jun '05

I'm trying to find the command which corresponds to SET DYNAMIC_COULOMB = ON. It seems to me that it should be energy_data.dynamic_coulomb = True, but when I try this, my log shows DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T; I interpret this to mean that it is off. When I use a top command file, I get: DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T T F T indicating that it is on. How do I get this to happen using a Python file? John Penniston

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Glycosylation on Asn
by John Simms 06 Jun '05

06 Jun '05

Hi All, I dont suppose that anyone has either a glycosylated Asn topology or a patch for the glycosylation on an asn that they are willing to give me. I am sorry its a bit cheeky Cheers John

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Clustering
by John Penniston 04 Jun '05

04 Jun '05

1 0

modeling a complex
by Edoardo Saccenti 03 Jun '05

03 Jun '05

Dear friends, I have a pdb file containing coordinates for a complex of two subunits: subunits 1 in chain A and subunits 2 in chain B chain C and D contains fragments of another molecule that I don't care. I want to model in the same time a molecule 1 on chain A and a molecule 2 on chain B so to build a model of the complex molecule1-molucule2 on the complex of the two subunits in the pdb file. In which way I have to write down align file? Tanks a lot Edoardo -- "Raffiniert ist der Herr Gott, aber boshaft ist Er nicht." --- Dr. Edoardo Saccenti CERM Nuclear Magnetic Resonance Research Center Scientific Pole - University of Florence Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) tel: +39 055 4574193 fax: +39 055 4574253 saccenti(a)cerm.unifi.it www.cerm.unifi.it

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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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