- modeller_usage - salilab.org

doutbs about file
by Amanda Moraes 22 Jul '08

22 Jul '08

Hello! My name is Amanda Maia and I´m a beginner using Modeller. I´m having some trouble finding the answers to my questions on the manual. Could you help me? I have a sequence that aligns (BLAST pdb)with various structures on PDB within an average identity of 35%. Since I need to use as much models as I can get, I´m writing a PIR file with 5 templates. But one (1MDY) has 2 chains (out of 4) that blast quotes (B and E). Do I have to make a PIR line to each one? And a pdb file for each one too? Example: >P1;molde1MDYB structureX:molde1MDYB:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00 ----------------------------------------------------------------------------------------------------------------------------TTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------* >P1;molde1MDYA structureX:molde1MDYA:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00 ----------------------------------------------------------------------------------------------------------------------MELKRKTTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------* Thank you in advance! Amanda Maia Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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Fwd: The results of your email commands
by 刘君 22 Jul '08

22 Jul '08

I don't understand. Done. ---------- Forwarded message ---------- From: <modeller_usage-bounces(a)salilab.org> Date: 2008/7/22 Subject: The results of your email commands To: snailliujun(a)gmail.com The results of your email command are provided below. Attached is your original message. - Unprocessed: byBteSBwZXJzb25hbAplbWFpbC4gSSBhcHByZWNpYXRlIHlvdXIgZmVlZGJhY2sgYXMgc29vbiBh cyBwb3NzaWJsZS4gT3Igd291bGQgeW91CnBsZWFzZSBjaGVjayB5b3VyIHN5c3RlbSBrZXJuZWwg b2YgeW91ciBzZXJ2ZXIsIG9yIHBlcmhhcHMgaXQncyBqdXN0IGEKcGVyc29uYWxseSBvcGVyYXRp bmcgbWlzdGFrZT8KCnNpbmNlcmVseSB5b3VycywKc25haWxsaXVqdW4KCgotLS0tLS0tLS0tIEZv cndhcmRlZCBtZXNzYWdlIC0tLS0tLS0tLS0KRnJvbTogTW9kZWxsZXIgQ2FyZXRha2VyIDxtb2Rl bGxlci1jYXJlQHNhbGlsYWIub3JnPgpEYXRlOiAyMDA4LzcvMTgKU3ViamVjdDogUmU6IFttb2Rl bGxlcl91c2FnZV0gYSBxdWVzdGlvbiBvbiBNT0RFTExFUiB1c2FnZQpUbzogSXZhbiBBbmlzaGNo ZW5rbyA8YW5pc2hjaGVua28uaXZhbkBnbWFpbC5jb20+CrOty82juiBtb2RlbGxlcl91c2FnZUBz YWxpbGFiLm9yZwoKCkl2YW4gQW5pc2hjaGVua28gd3JvdGU6Cj4gSSBkZWFsIHdpdGggYSBwZXB0 aWRlICgzNSByZXNpZHVlcyBsb25nKS4gSSBrbm93IGl0cyBhbWlubyBhY2lkIHNlcXVlbmNlCj4g YW5kIGEgc2V0IG9mIG1lYW4gdmFsdWVzIGZvciBwaGktIGFuZCBwc2ktIGRpaGVkcmFscyBhbmQg dGhlIHJlc3BlY3RpdmUKPiBjb25maWRlbmNlIGludGVydmFsIGZvciBlYWNoIGRpaGVkcmFsIGFu Z2xlLiBUaGUgZGF0YSBpcyBvYnRhaW5lZCBmcm9tCj4gdGhlIE5NUiBleHBlcmltZW50cy4gVGhl IGFpbSBpcyB0byBvYnRhaW4gYSBzdHJ1Y3R1cmUgd2l0aCB0aGUKPiBtYWluLWNoYWluIGRpaGVk cmFscyBseWluZyB3aXRoaW4gdGhlIGNvcnJlc3BvbmRpbmcgY29uZmlkZW5jZSBpbnRlcnZhbAo+ IGZvciBldmVyeSByZXNpZHVlLiBTaWRlIGNoYWlucyBjYW4gdGFrZSBhbnkgY29uZm9ybWF0aW9u LiBIb3cgY2FuIHN1Y2gKPiByZXN0cmFpbnRzIGJlIGRlc2NyaWJlZCBpbiBNT0RFTExFUj8KCjEu IFJlYWQgaW4gdGhlIGluaXRpYWwgc3RydWN0dXJlIChzZWUgdGhlIG1hbnVhbCBmb3IgY29tcGxl dGVfcGRiKSBvcgpidWlsZCBhbiBleHRlbmRlZCBjaGFpbiBmcm9tIHRoZSBBQSBzZXF1ZW5jZSAo bW9kZWwuYnVpbGRfc2VxdWVuY2UpLgoKMi4gQWRkIHJlc3RyYWludHMgb24gZWFjaCBkaWhlZHJh bC4gU2VlIFJlc3RyYWludHMuYWRkLiBUbyBnZXQgdGhlIGxpc3QKb2YgYXRvbXMgZm9yIGVhY2gg ZGloZWRyYWwgdHlwZSBpbiBlYWNoIHJlc2lkdWUsIHNlZSBSZXNpZHVlLnBoaSBhbmQKRGloZWRy YWwuYXRvbXMuIEZvciBleGFtcGxlLCB0byBjb25zdHJhaW4gZXZlcnkgcGhpIGFuZ2xlIGluIHRo ZSBtb2RlbAonbScgdG8gMCArLy0gMC4xIHJhZGlhbnMsIHVzaW5nIGEgR2F1c3NpYW4gcmVzdHJh - Ignored: aW50OgoKZm9yIHJlcyBpbiBtLnJlc2lkdWVzOgogICAgaWYgcmVzLnBoaSBpcyBub3QgTm9uZToK ICAgICAgICBhdG9tcyA9IHJlcy5waGkuYXRvbXMKICAgICAgICBmID0gZm9ybXMuZ2F1c3NpYW4o Z3JvdXA9cGh5c2ljYWwuZGloZWRyYWwsCiAgICAgICAgICAgICAgICAgICAgICAgICAgIGZlYXR1 cmU9ZmVhdHVyZXMuZGloZWRyYWwoKmF0b21zKSwKICAgICAgICAgICAgICAgICAgICAgICAgICAg bWVhbj0wLCBzdGRldj0wLjEpCiAgICAgICAgbS5yZXN0cmFpbnRzLmFkZChmKQoKMy4gWW91IG1h eSBhbHNvIHdhbnQgdG8gYnVpbGQgb3RoZXIgc2V0cyBvZiByZXN0cmFpbnRzLCBmb3IgZXhhbXBs ZQpzdGVyZW9jaGVtaWNhbCByZXN0cmFpbnRzLiBTZWUgUmVzdHJhaW50cy5tYWtlLgoKNC4gT3B0 aW1pemUgdGhlIHN0cnVjdHVyZS4gU2VlIGNvbmp1Z2F0ZV9ncmFkaWVudHMoKS4KCiAgICAgICBC ZW4gV2ViYiwgTW9kZWxsZXIgQ2FyZXRha2VyCi0tCm1vZGVsbGVyLWNhcmVAc2FsaWxhYi5vcmcg ICAgICAgICAgICAgaHR0cDovL3d3dy5zYWxpbGFiLm9yZy9tb2RlbGxlci8KTW9kZWxsZXIgbWFp bCBsaXN0OiBodHRwOi8vc2FsaWxhYi5vcmcvbWFpbG1hbi9saXN0aW5mby9tb2RlbGxlcl91c2Fn ZQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwptb2RlbGxl cl91c2FnZSBtYWlsaW5nIGxpc3QKbW9kZWxsZXJfdXNhZ2VAc2FsaWxhYi5vcmcKaHR0cHM6Ly9z YWxpbGFiLm9yZy9tYWlsbWFuL2xpc3RpbmZvL21vZGVsbGVyX3VzYWdlCgoKCi0tIApUb21vcnJv dyBpcyBhbm90aGVyIGRheS4K - Done. ---------- 已转发邮件 ---------- From: "刘君" <snailliujun(a)gmail.com> To: modeller_usage-request(a)salilab.org Date: Tue, 22 Jul 2008 23:55:40 +0800 Subject: Fwd: [modeller_usage] a question on MODELLER usage I guess how these users' questions and your reply turns to my personal email. I appreciate your feedback as soon as possible. Or would you please check your system kernel of your server, or perhaps it's just a personally operating mistake? sincerely yours, snailliujun ---------- Forwarded message ---------- From: Modeller Caretaker <modeller-care(a)salilab.org> Date: 2008/7/18 Subject: Re: [modeller_usage] a question on MODELLER usage To: Ivan Anishchenko <anishchenko.ivan(a)gmail.com> 抄送： modeller_usage(a)salilab.org Ivan Anishchenko wrote: > I deal with a peptide (35 residues long). I know its amino acid sequence > and a set of mean values for phi- and psi- dihedrals and the respective > confidence interval for each dihedral angle. The data is obtained from > the NMR experiments. The aim is to obtain a structure with the > main-chain dihedrals lying within the corresponding confidence interval > for every residue. Side chains can take any conformation. How can such > restraints be described in MODELLER? 1. Read in the initial structure (see the manual for complete_pdb) or build an extended chain from the AA sequence (model.build_sequence). 2. Add restraints on each dihedral. See Restraints.add. To get the list of atoms for each dihedral type in each residue, see Residue.phi and Dihedral.atoms. For example, to constrain every phi angle in the model 'm' to 0 +/- 0.1 radians, using a Gaussian restraint: for res in m.residues: if res.phi is not None: atoms = res.phi.atoms f = forms.gaussian(group=physical.dihedral, feature=features.dihedral(*atoms), mean=0, stdev=0.1) m.restraints.add(f) 3. You may also want to build other sets of restraints, for example stereochemical restraints. See Restraints.make. 4. Optimize the structure. See conjugate_gradients(). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage -- Tomorrow is another day. -- Tomorrow is another day.

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a question on MODELLER usage
by Ivan Anishchenko 22 Jul '08

22 Jul '08

Hello, I deal with a peptide (35 residues long). I know its amino acid sequence and a set of mean values for phi- and psi- dihedrals and the respective confidence interval for each dihedral angle. The data is obtained from the NMR experiments. The aim is to obtain a structure with the main-chain dihedrals lying within the corresponding confidence interval for every residue. Side chains can take any conformation. How can such restraints be described in MODELLER? Thanks beforehand! -- Yours sincerely, Ivan V. Anishchenko

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Installation on Debian Linux
by Francesco Pietra 22 Jul '08

22 Jul '08

As a Debian Linux user I found difficult to abandon the Debian packaging system. Therefore, to Install Modeller 9v4-1 I first converted the rpm to deb with alien (flags -k --scripts. Then I installed the deb package with dpkg (flag -i). The command reports that the package is installed but requires a password, indicating which configuration file to edit to set the password. That way, you avoid possible blurring of the OS by going through an rpm; deb positions every file at the expected place; you have the modeller command on path; you have full command of packaging in case of installations of new version. If not already posted by other members, it might be useful, though I understand that Debian (curiously) is not popular in USA. Cheers -- Dr Francesco Pietra Professor of Chemistry Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594 Palazzo Ducale 55100 Lucca (Italy)

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symmetric hexamer
by o.h.weiergraeber＠fz-juelich.de 16 Jul '08

16 Jul '08

Hello, we are trying to build a symmetric hexamer of a 735 aa protein molecule. Modelling the monomer works without problems. For the hexamer, we have generated the hexameric template and replicated the target sequence in the alignment file accordingly. This works flawlessly, as well. However, if we insert these symmetry retraints (adopted from the example in the manual) ------------------------------------------- # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) ------------------------------------------- leaving both alignment and template files untouched, then the program stops with the following error: ------------------------------------------- Traceback (most recent call last): File "get-model2.py", line 42, in ? a.make() # do homology modeling File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 436, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 524, in mkhomcsr self.special_restraints(aln) File "get-model2.py", line 23, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) TypeError: __init__() takes exactly 4 arguments (8 given) ------------------------------------------- We are a bit lost here :( Which init call is the message referring to? Any ideas how to resolve this? Oliver ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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GA341 assessment
by Lella Sana 02 Jul '08

02 Jul '08

Dear all, how could I carry out GA341 assessment on a model not produced by MODELLER but by an ab initio method? I'm using MODELLER 9v2. Thanx in advance Hai un indirizzo email difficile da ricordare? Scegli quello che hai sempre desiderato su Yahoo! Mail http://it.docs.yahoo.com/nuovo_indirizzo.html

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restraint check
by Ryan 01 Jul '08

01 Jul '08

I am currently modelling a system with a fair amount of restraints (symmetry, secondary structure, and distance) that takes over an hour to model. I have found that if i make a mistake in naming one of the residues/atoms in one of my restraints, that the program does not catch this right away, but will crash after about an hour when it finally notices that the restraint is invalid. This is a pretty inconvenient way in realizing my input mistakes, and am wondering if there is a way to have Modeller check that all of my restraints are valid before the program begins processing the models. Thanks, ryan

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non-proline cis-peptide bonds
by François Sampieri 01 Jul '08

01 Jul '08

Hi all, I want to force a non-proline peptide bond to the cis configuration in a 64-residue model. I found a routine to force Pro residue to the cis configuration in the FAQ. I assumed that it would not make a difference if the residue it applies to is not an actual proline and I include the routine in my .py script, but I got only models with the trans peptide configuration. This is an example of my .py file : # Homology modelling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 12 and 63: self.patch(residue_type='DISU', residues=(self.residues['12'], self.residues['63'])) # A disulfide between residues 16 and 36: self.patch(residue_type='DISU', residues=(self.residues['16'], self.residues['36'])) # A disulfide between residues 22 and 46: self.patch(residue_type='DISU', residues=(self.residues['22'], self.residues['46'])) # A disulfide between residues 26 and 48: self.patch(residue_type='DISU', residues=(self.residues['26'], self.residues['48'])) # Redefine the special_restraints routine to force Pro to cis conformation: # (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): a = self.atoms cispeptide(self.restraints, atom_ids1=(a['O:9'], a['C:9'], a['N:10'], a['CA:10']), atom_ids2=(a['CA:9'], a['C:9'], a['N:10'], a['CA:10'])) 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 = automodel(env, alnfile = 'AahII-cis.ali', # alignment filename knowns = '1PTX', # codes of the templates sequence = 'AahII-cis') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling ---------------------------------------------------------------------------------------------- I noticed only 3 lines in the log file with warnings: ... getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C +N atom indices : 503 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C CA +N O atom indices : 503 496 0 504 ... 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. ... ---------------------------------------------------------------------------------------------- Please could somebody tell me what is wrong in this modeling? Thank you! Regards, François Sampieri

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question about mutate_model
by Anna Marabotti 30 Jun '08

30 Jun '08

I would like to use the script mutate_model to evaluate different conformations of the same mutant side chain inserted in a protein. Therefore I used the script "mutate model" as suggested in the Wiki section, and repeated the procedure 5 times, expecting to obtain 5 different conformations of the mutant side chain. Instead, I obtained 5 identical proteins with side chains perfectly superimposable between each others. How can I manage myself in order to obtain 5 different models of the same mutation? Moreover, this is probably a naive question, but since repeated MD cycles generally do not produce identical results, why this protocol did not work in such a way? Many thanks and best regards Anna Marabotti ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti(a)isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna.htm Funded by RNBIO: http://www.rnbio.it/ ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

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Parallel job (part 2)
by Francesco Musiani 17 Jun '08

17 Jun '08

Ok, I modified my script as in the example. ---- (script) from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) log.verbose() class mymodel(allhmodel): def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = environ() env.io_atom_files_directory = './' a = mymodel(env, alnfile = 'HpUreE.ali', knowns = 'dimerBp', sequence = 'HpUreE', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.use_parallel_job(j) a.make() # Output data ok_models = filter(lambda x: x['failure'] is None, a.outputs) key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # read model file mdl = complete_pdb(env, m['name']) # Assess with DOPE: s = selection(mdl) s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='HpUreE.best.profile', normalize_profile=True, smoothing_window=15) ---- (end) i obtained this error: ---- (log) Traceback (most recent call last): File "HpUreE.py", line 40, in ? a.make() File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 109, in make self.multiple_models(atmsel) File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 213, in multiple_models self.parallel_multiple_models(atmsel) File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 233, in parallel_multiple_models self.outputs.extend(job.run_all_tasks()) File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 110, in run_all_tasks self.finish_next_task() File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 127, in finish_next_task self.process_event(obj, s) File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 141, in process_event task = obj.task_results() File "/work/programs/MODELLER/modlib/modeller/parallel/slave.py", line 54, in task_results r = self.get_data(allow_heartbeat=True) File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 81, in get_data (cmdtype, obj) = self._recv() File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 119, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'mymodel' from <Slave on localhost> ---- (end) in the .slave0 and .slave1 log file I have this error: ---- (log) Slave startup: connect to master at 127.0.1.1:59037:0:EABQEAKC Traceback (most recent call last): File "<string>", line 1, in ? File "/work/programs/MODELLER/modlib/modeller/parallel/slaveloop.py", line 63, in slaveloop handle_slave_io(master, slavedict) File "/work/programs/MODELLER/modlib/modeller/parallel/slaveloop.py", line 38, in handle_slave_io exec(cmdstr, slavedict) File "<string>", line 1, in ? File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 81, in get_data (cmdtype, obj) = self._recv() File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 117, in _recv (obj, self.buffer) = cmdtype.recv(self.buffer) File "/work/programs/MODELLER/modlib/modeller/parallel/data_types.py", line 71, in recv return (pickle.loads(obj), buffer[1+p.get_position():]) File "/usr/local/lib/python2.3/pickle.py", line 1394, in loads return Unpickler(file).load() File "/usr/local/lib/python2.3/pickle.py", line 872, in load dispatch[key](self) File "/usr/local/lib/python2.3/pickle.py", line 1104, in load_global klass = self.find_class(module, name) File "/usr/local/lib/python2.3/pickle.py", line 1140, in find_class klass = getattr(mod, name) AttributeError: 'module' object has no attribute 'mymodel' ---- (end) running Modeller in the normal way do not produce any error. Thanks Francesco --- Francesco Musiani francesco.musiani(a)unibo.it ---

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