- modeller_usage - salilab.org

h-bonds with loop models
by David Gell 30 Jun '07

30 Jun '07

Dear modellers i am trying to build models for a single missing loop on a known xtal structure and i have a couple of questions 1) can modeller introduce hydrogen bonds in loop modelling (is it true that all-hydrogen models are not fully implemented for loop modelling)? 2) is it true that modeller does not include hydrophobic packing factors? i currently have models with fully exposed hydrophobics that have similar 'modeller objective function' to those with more buried hydrophobic sidechains. i'm a modeller newbie, and above is based on my understanding (i.e. likely flawed) of the mail archives and docs. perhaps i should be introducing some 'artificial' distance restraints to mimic the effects of the above interactions? any advice greatly received. cheers dave gell

2 1

setting restyp, top_heav and par libs
by David Marshall 30 Jun '07

30 Jun '07

Dear Modellers, I am currently trying to model the effect of phosphorylation on a protein. I have been kindly provided with adapted top_heav.lib and par.lib files and I have modified restyp.lib accordingly. I have searched the manual but cannot find commands to set these .lib files in my .py files. I want to avoid overwriting the existing files as I do not have access. Many thanks for your time, David Marshall

2 1

what should PYTHONPATH and LD_LIBRARY_PATH be set to?
by David Mobley 27 Jun '07

27 Jun '07

Hi, Sorry to ask such an apparently naive question, but I haven't been able to find the answer on the mailing list, or in the documentation, or by experimenting myself... In a generic linux installation, when I'm not using an RPM, what do I need to set the PYTHONPATH and LD_LIBRARY_PATH to, in order to be able to use modeller in the typical python way (i.e. "import modeller" from within python)? The documentation indicates this is possible with modeller 9v1, if the above paths are set appropriately, but it doesn't indicate what "appropriately" means. Thanks! David

2 1

modelling a chimera from structureM-type templates
by Cahya Prihatna 27 Jun '07

27 Jun '07

I want to model a chimera protein which consists of two individual proteins. The crystallography of these proteins have not been reported, I was only able to find the model for them. How can I build the chimera based on models as templates? Regards, Cahya Prihatna

2 1

build_profile.py help
by Eeson Rajendra 27 Jun '07

27 Jun '07

Hi I have a sequence that I want to check against known structures and am trying to run "build_profile.py". I get an error: ************** 'import site' failed; use -v for traceback Traceback (most recent call last): File "build_profile.py", line 10, in ? chains_list='ALL', minmax_db_seq_len=(1, 40000), clean_sequences=True) File "C:\Program Files\Modeller9v1\modlib\modeller\sequence_db.py", line 48, i n read minmax_db_seq_len) IOError: openf______E> Cannot open file pdb95.fsa: No such file or directory ************* The pdb95.fsa file is located in my Modeller9v1\examples\commands folder. Should it be moved? Additionally, I have downloaded the pdb_95.cod.gz, pdb_40.cod.gz and pdball.pir.gz files. I have unzipped them but am not sure which directory to place them in (or the files that they replace). Do I need to change their file extensions? Is pdb_95.cod the pdb95.bin file referenced in the example build_profile.py script? Any help would be appreciated. Eeson

2 1

model.energy()
by Jayapal, Prabha 27 Jun '07

27 Jun '07

Dear All: I am a new user of MODELLER 9. I got an appreciable model using modeller and I would like to evaluate the model by the model.energy(). But I got an error like, runcmd______> topology.append(file='$(LIB)/top_heav.lib') read_to_681_> topology.submodel read from topology file: 3 runcmd______> parameters.append(file='$(LIB)/par.lib') runcmd______> model.read(file='nitro.B99990066', (def)model_format='PDB', (def)model_segment=('FIRST:@', 'LAST:')) runcmd______> alignment.append_model(atom_files='nitro.B99990066', align_codes='nitro.B99990066') runcmd______> alignment.append_model(atom_files='nitro.B99990066.ini', align_codes='nitro.B99990066-ini') runcmd______> model.generate_topology((def)patch_default=True) getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C +N atom indices : 880 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C CA +N O atom indices : 880 875 0 881 runcmd______> model.transfer_xyz((def)cluster_cut=-1.0, (def)cluster_method='RMSD') transfe_507E> Number of residues in alignment different from that in MODEL: 60 120 (Did you call clear_topology() before generate_topology() ?) The top file is, # Example for: model.energy() # This will calculate the stereochemical energy (bonds, # angles, dihedrals, impropers) for a given model. env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env) code = "nitro.B99990066" mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini') mdl.generate_topology(aln[code+'-ini']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) molpdf = mdl.energy(edat=energy_data(dynamic_sphere=True)) Could any body help me with this? I used PROCHECK and found 90% of residue resides in core area ie most favoured. Thank you in advance Cheers J.Prabha

2 1

Sequence alignment softwares
by DPF Chocolate 26 Jun '07

26 Jun '07

Hi, I have got some exprience on modeller using InsightII software. I used to do sequence alignment using InsightII software. If I want to do sequence alignment without InsightII, how can I do that. Are there any free sequence alignment softwares (GUI) available, so that we can save ".pir" file and give that file to modeller. -- Regards, JOCKY

1 0

homology problem
by Fabian Glaser 14 Jun '07

14 Jun '07

Hello all, I am recently became interested in modeling, and I am trying to model a recently discovered protein, that unfortunately appears not to have homologues at all. I tried to run the molecule domain by domain, try to use GenTHREADER, 3DPSSM and several others methods and metaservers to find homologues, but nothing gives an alignment with a reasonable accuracy or p-value. Could somebody recommend me what to do in this case to obtain a reasonable alignment / model? Any suggestion will be highly appreciated. Best regards, Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: *fglaser(a)tx.technion.ac.il* <fglaser(a)tx.technion.ac.il> Tel: +972-4-829-3701

1 0

help--model-segment.py
by jinlian05＠lzu.cn 06 Jun '07

06 Jun '07

Hi: I use 'model-segment.py' to build the structure of my target protein, the following is the script: from modeller import * from modeller.automodel import * log.verbose() class mymodel(automodel): def select_atoms(mdl): return selection(mdl.residue_range('37:A','63:A'), mdl.residue_range('74:A','96:A'), mdl.residue_range('111:A','133:A'), mdl.residue_range('153:A','173:A'), mdl.residue_range('203:A','224:A'), mdl.residue_range('250:A','274:A'), mdl.residue_range('287:A','308:A')) env=environ() env.io.atoms_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knowns='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make() after running the scripts, it appears some errors: Traceback (most recent call last): File "selection.py", line 22, in ? a.make() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 118, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 483, in _check_select_atoms atmsel = self.select_atoms() File "selection.py", line 6, in select_atoms return selection(mdl.residue_range('37:A','63:A'), File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 37:A' The residue numbers in the model are really the same as residue numbers in the template. After 'mod9v1 model-segment.py', it produce the 'tm-mrg.ini' and 'tm-mrg.scr'files, if the script is wrong, dose it produce results else? ps: is there any diffference between the .ini files and .pdb files?

2 1

modweb
by James Fethiere 05 Jun '07

05 Jun '07

Hi, is there a way to tell modweb to use a specific pdb as template instead of the one he finds by itself. Thanks james

1 0