June 2005 - modeller_usage

N-terminal acetylation via 'automodel?' ?
by Niels Johan Christensen 24 Jun '05

24 Jun '05

Dear all, I am a MODELLER newbie, modelling a synthetic peptide (3 chains * 30 AAs) from the 1COI.PDB entry. The results produced by the 'automodel' class are in many ways satisfactory, however I cannot figure out how to acetylate the amino terminus of the peptide. I acknowledge that this problem is adressed in the MODELLER FAQ, however the solution provided there does not seem to be designed for use with a simple 'automodel' script such as: from modeller.automodel import * env = environ() a = automodel(env, alnfile='vald-tril16c-hand.pir', knowns='merged.pdb', sequence='TRIL16C') a.starting_model = 1 a.ending_model = 5 a.make() Hence my question is: Will I have to abandon the use of the 'automodel' class and gain more insight into MODELLERs "fine structure" in order to change the default terminus patching ? Thank you. Best Regards, Niels Johan Christensen

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Homology model at specific pH
by Panapat Uawithya 23 Jun '05

23 Jun '05

Hi, I want to see the effect of the pH and the protein model. How can I model protein at specific pH. e.g. I want to see the + or - charge effect of histidine upon protein structure. Panapat --------------------------------- Yahoo! Mail Stay connected, organized, and protected. Take the tour

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not generating pdb files
by gerald.quon＠utoronto.ca 23 Jun '05

23 Jun '05

Hi, I'm running modeller 8v0, and am trying to model 2 different proteins on the same template. For some reason, for one of the alignments (#1), the only output being produced is the .D* and .V* files - the models aren't being generated (and the D* and V* files are being produced quite quickly). For alignment #2, I'm getting the models out so that isn't a problem. Any help would be appreciated...the same commands are being used for both alignments, which i've shown below.. Gerald ------------ script command: def my_model(_alnfile, _knowns, _sequence): log.verbose() #request verbose output env = environ() #create a new MODELLER environment to build model env.io.atom_files_directory = './:../pdb/' a = automodel (env, alnfile = _alnfile, knowns = _knowns, sequence = _sequence) a.starting_model = 1 a.ending_model = 50 a.final_malign3d = True a.md_level = refine.slow a.make() ----------- alignment #1: >P1;1PVM structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00 KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/ KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS * >P1;a1 sequence:: : : : :::-1.00:-1.00 DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE/ DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE * ------------------------------ Alignment #2: >P1;1PVM structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00 KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/ KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS * >P1;a2 sequence:: : : : :::-1.00:-1.00 RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR RDLIISIENARKKQDGVV------------------------------------------ ------------------------------------------------------------ -------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA/ RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR RDLIISIENARKKQDGVV------------------------------------------ ------------------------------------------------------------ -------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA *

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disulfide bonds
by Dmitry Osolodkin 23 Jun '05

23 Jun '05

Hi all, I have a little problem with Modeller 8v0. Usually it patches disulfide bonds automatically. But when I try to make model of my protein, it patches only one disulfide instead of five. When I try to define these bonds manually (like in FAQ p.3), the procedure stops and says: TypeError: special_patches() takes exactly 1 argument (2 given) .log file ends immediately. What can be the root of problem? Input files are here. The template is a protein with pdb id 1yi5, slightly minimized in Sybyl. When I use pdb id 1ux2 as a template, there are no problems, and disulfide bonds are on their place. >P1;1yi5_min structureX:1yi5_min:.:A:.:E: : : : LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTT-N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKGR/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTTEN-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT--N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ * >P1;r1 sequence:r1:.:A:.:E: : : : PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ * # Homology modelling by the automodel class 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 = './' a = allhmodel(env, alnfile = 'align.ali', # alignment filename knowns = '1yi5_min', # codes of the templates sequence = 'r1') # code of the target # Very thorough VTFM optimization: a.library_schedule = 1 a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # do the actual homology modelling

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Modeller 8v1 release
by Modeller Caretaker 22 Jun '05

22 Jun '05

The new version of Modeller, 8v1, is now available for download from http://salilab.org/modeller/. If you have a license key for Modeller 8v0 or 7v7, there is no need to reregister for Modeller 8v1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) If you encounter bugs in Modeller 8v1, please see http://salilab.org/modeller/manual/node11.html for information on how to report them. New features in Modeller 8v1 include: # Removal of limits on the number of pseudo atoms, segments, the length of file names and most other strings, and the number of parameters in parameter files. # Removal of the read_restyp() command. To read a user-defined residue type file, set restyp_lib_file when creating an environ object. # Bug fix: the correct VDW radii (as selected by topology.submodel) are now used for PSA calculations (previously the all-hydrogen radii were used in all cases). # Improved error handling: almost all errors should be recoverable now (using the standard Python exception handling mechanism) and incorrect input should trigger an error rather than causing Modeller to crash (please report any crashes as bugs to the developers). # SALIGN bug fixes, improved binning of access classes. # Modeller scripts are now more like 'real' Python scripts; the PYTHONPATH environment variable is honored, and additional command line arguments can be given to your scripts (accessible as sys.argv). # Bug fix for alignment.segment_matching(): correct alignment scores are now written. # Support for AMD64 and EM64T (Opteron/Xeon64) Linux machines. # DOPE model assessment now returns only the DOPE energy itself by default, ignoring other energy terms. # Bug fix for model.restraints.pick() when used with absolute position restraints; always allow 1-atom restraints to pass the residue_span_range check. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Pick Restraints
by John Penniston 16 Jun '05

16 Jun '05

2 1

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

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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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