October 2009 - modeller_usage

Basic tutorial
by Marco 03 Nov '09

03 Nov '09

Dear all, I'm following the basic tutorial and I have a couple of question: a) some times ago Modeller grouped similar structures and scanned against the representative protein of each group: is this still valid? b) where I find the data on cristallografic resolution of the chosen proteins? The pdball.pir file does not contain this data. Thanks for your help, Marco

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Basic tutorial
by Marco 31 Oct '09

31 Oct '09

Dear all, I'm following the basic tutorial and I have a couple of question: a) some times ago Modeller grouped similar structures and scanned against the representative protein of each group: is this still valid? b) where I find the data on cristallografic resolution of the chosen proteins? The pdball.pir file does not contains this data. Thanks for your help, Marco

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Re: [modeller_usage] Bad Contacts and Dimeric symmetry
by nornik 28 Oct '09

28 Oct '09

Hello again. I am now making new models with only symmetry restraints on the alpha carbons. However, I still think it's strange that when i have a model with 26 or even 38 bad clashes they are all 2.5 or 2.6 Å. Do you know why this is? Another thing is that the alignment should not be poor. There are only three small deletions and one large insert and they are all in surface exposed loop regions. My alignment has a 57 % identity so it could not be drastically changed. I also do not think that the bad contacts are in positions close to the deletions/inserts and moving these would greatly decrease the % identity. I guess I could use just my automodel models since they are rather good but the template is fully symmetric and it's for my Master's thesis so I want to do as nice models as possible. Thank you for putting such effort in helping all of us /Niklas

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Permission denied message
by Manoel Arcisio-Miranda 28 Oct '09

28 Oct '09

Dear Ben, I am beginner in modeling of proteins. I downloaded the Modeller 9v7 (Windows package) and I am following the tutorials. I just started the Basic Modeling tutorial, but when I type any command at the command line, for example: mod9v7 build_profile.py, the following message appear: Cannot open logfile build_profile.log: Permission denied I also tried to run the command: mod9v7 model.py. and I got the same message. I downloaded all input and output files for this tutorial. So, what should I do? P.S.: the list of systems that I am using: Windows Vista, Modeller 9v7 and Phython 2.3.5 Thanks so much, Manoel ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Stop renumbering of new model
by João Rodrigues 26 Oct '09

26 Oct '09

Dear all, When MODELLER creates a new model, it renumbers it. The first residue is 1, second is 2, etc. How can I force these residues to obey the original template numbering? Say, if the template starts at residue 54, MODELLER's models will start with 54? Regards! João [ .. ] Rodrigues (Blog) http://doeidoei.wordpress.com (MSN) always_asleep_(a)hotmail.com (Skype) rodrigues.jglm

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Model missing residues in a trimer
by Panagiotis Kastritis 26 Oct '09

26 Oct '09

Dear all, I would like to ask you how is it possible to model missing residues in a trimer that I have. All the monomers have missing residues and each chain has numbering from 1 to 100 let's say. I searched the archive but I haven't found such question. I can try this one /from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('133', '135'), self.residue_range('216', '230')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '1qg8', sequence = '1qg8_fill') a.starting_model= 1 a.ending_model = 1 a.make() /but how can I expand it to more than one chain? I would like only to fill the missing residues, with only local minimization of the structure and not global. Is it possible to do it in modeller? Thank you in advance, Panagiotis

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Bad Contacts and Dimeric symmetry
by nornik 26 Oct '09

26 Oct '09

My first issue is about bad contacts. When i produce models and evaluate them with procheck I always get some bad contacts. I have checked the procheck output files and noticed that all bad contacts always have a distance of 2.5 or 2.6 angstroms. Is there any way to change the minimum distance between atoms (i.e. increasing the different atom radii), since it seems like modeller and procheck have different opinions about what a bad contact is? My second issue is about dimeric symmetry. I produced a model of a dimer using the automodel class and got some nice models. Then i wanted to produce the dimers with symmetry restraints and got many angles in disallowed regions, many bad contacts and very low G-factors. This seems very strange since the only difference between my two runs was that i requested symmetry in my second run. Why do my symmetrical dimers become so bad? These are my two different scripts: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='model-template.ali', knowns='template', sequence='model', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 100 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.slow a.make() ------------------------------------------------- from modeller import * from modeller.automodel import * log.verbose() class MyModel(automodel): 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() a = MyModel(env, alnfile='chron1-2OBT.ali', knowns='2OBT', sequence='chron1', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 100 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.slow a.make() Thank you /Niklas

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ERROR ALIGN_CODES
by Leonardo Herrera 26 Oct '09

26 Oct '09

Hi modeller user's I have a problem when I am realising my model with multiple templates, in the step to align the alignment of pdb's versus my sequence I obtain the following problem… raceback (most recent call last): File "align2d_mult.py", line 14, in <module> aln.append(file='Tc30.ali', align_codes='giAAR00925') File "/usr/lib/python2.6/site-packages/modeller/alignment.py", line 79, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 13) = giAAR00925 I could'nt find an answer to this problem, it already changes the format (fasta to pir ...), and code several times (giAAR00925 to 13... to c30 ...), so please can somebody help with this error message? Thanks in advance My script is from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned structure(s): aln = alignment(env) aln.append(file='alineamiento.ali', align_codes='all') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='Tc30.ali', align_codes='giAAR00925') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(output='', max_gap_length=20, gap_function=True, # to use structure-dependent gap penalty alignment_type='PAIRWISE', align_block=aln_block, feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0, gap_penalties_1d=(-450, 0), gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.), similarity_flag=True) aln.write(file='Tc30-mult.ali', alignment_format='PIR') aln.write(file='Tc30-mult.pap', alignment_format='PAP') my file Tc30.ali is >P1;giAAR00925 giAAR00925 524 residues MGRLQRFSAFVPLTLSFISQASAAIGPVTDLTISDADISPDGFTRAAVVMNDQFPGPLIAGNKGDNFQINVI DNLSNSTMLTSTTIHWHGFFQKGTNWADGAAFVNQCPISAGNSFLYDFTATDQAGTFWYHSHLSTQYCDGLR GPMVVYDPDDPHASLYDVDDDSTVITLSDWYHTAARLGARFPAGADSTLINGLGRAAGGDADAALAVFNVTQ GSRYRFRLVSLSCDPNFNFTIQDHNMTIIEVDGVNVEPVTVDSIQIFAGQRYSFVLTADQDIGNYWIQAVPN TGTVTTDGGVNSAILRYDTADPIEPDAADPTSSIPLVETDLVPLENLAAPGDPTVGGVDLAMNLEFDFNGTW FFINGEPFVPPSVPVLLQIMSGAQSAADLLPSGSVYTLPANSTIEISFPMNTTAAPGAPHPFHLHGHTFYVV RSAGSTEYNYVNPPQRDTVSTGTDGDNVTIRFTTNNPGPWFLHCHIDFHLDAGFAIVLSEDTPDAASANTPS SAWDDLCPTYNTDYPDGLGR* and my alineamiento.ali is >P1;1gw0.10wA structureX:1gw0.10w_fit.pdb: 1 :A:+573 :A:::-1.00:-1.00 --EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANW GDTVEVTVINNLV----TNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRAR-QYGTSWYHSHFSA QYGNGVVGTIQING---PASLPYDID--LGVFPITDYYYRAADDLVHFTQN-----NAPPFSDNVLINGTAVNPN TGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAP -DNYWFNVTFGGQAACGG-----SLNPH----PAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSV-- PVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGN------TSYPVSDNIVQVDAVDQWT YWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQ-RFVFDPAVDLARLNGDNPPRRDTTMLPAG---GW LLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL-- ----------------------....wwwwwwwwww* >P1;1gyc.10wA structureX:1gyc.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 AI--------------------------------GPAASLVVANA--PVSPDG-FLRDAIVVNGVFPSPLITGKK GDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIAS-GHSFLYDFHVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPR----------FPLGADATLINGLGRSAS TPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTV -GNYWIRANPN--F---------GTVGFAGGINSAILRYQGAPVAEPTTTQTTS-VIP-LIETNLHPLARMPVPG SPTPGGVDKALNLAFNFNG-----TNFFINNASFTPP-TVPVLLQILSG---AQTAQDLLPAGSVYPLP-AHSTI EITLPATA-LAPGAPHPFHLHGHAFAVVRSAGS----------------T--TYNYNDPIFRDVVSTGTPAAGDN VTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAA--NPVPKAWSDLCPIYDGLSEANQ---------- ----------------------....wwwwwwwwww* >P1;1kya.10wA structureX:1kya.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 GI--------------------------------GPVADLTITNA--AVSPDG-FSRQAVVVNGGTPGPLITGNM GDRFQLNVIDNLTNHTMLKSTSIHWHGFFQKGTNWADGPAFINQCPISS-GHSFLYDFQVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPNDPAADLYDVDNDDTVITLVDWYHVAAKLGPA----------FPLGADATLINGKGRSPS TTTADLSVISVTPGKRYRFRLVSLSCDPNYTFSIDGHNMTIIETDSINTAPLVVDSIQIFAAQRYSFVLEANQAV -DNYWIRANPN--F---------GNVGFTGGINSAILRYDGAAAVEPTTTQTTS-TAP-LNEVNLHPLVATAVPG SPVAGGVDLAINMAFNFNG-----TNFFINGASFTPP-TVPVLLQIISG---AQNAQDLLPSGSVYSLP-SNADI EISFPATA-AAPGAPHPFHLHGHAFAVVRSAGS----------------T--VYNYDNPIFRDVVSTGTPAAGDN VTIRFRTDNPGPWFLHCHIDFHLEAGFAVVFAEDIPDVASA--NPVPQAWSDLCPTYDARDPSDQ---------- ----------------------....wwwwwwwwww* -- MenB Leonardo David Herrera Zúñiga POSGRADO EN QUÍMICA UAMI Biofisicoquímica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674

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Help with mutation!
by tianjian3721 26 Oct '09

26 Oct '09

Hi, I want to use modeller to mutate the selected residues and obtain multiply models. But modeller usually give just one model. Then would you tell me how to redesign the python to generate multiply models? Here is the script that I have used to generate the mutant. Thanks in advance! Jian # Example for: selection.mutate() from modeller import * env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = "t_str.pdb" aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) sel_1 = selection(mdl.residues["40:A"]) sel_1.mutate(residue_type="SER") aln.append_model(mdl, align_codes="1fas-1") mdl.clear_topology() mdl.generate_topology(aln['1fas-1']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file="4lyzT40S_S91V.pdb")

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Re: [modeller_usage] ERROR ALIGN_CODES
by nornik 23 Oct '09

23 Oct '09

Hello Leonardo My first guess would be that the Tc30.ali file is impossible for Modeller to interpret. In the tutorial example the .ali file has the following format: >P1;TvLDH sequence:TvLDH:::::::0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWI... But then again you say that you have tried the PIR format. However, the error message implies that it cannot read the sequence for giAAR00925. Have you tried to just change the Tc30.ali file to: >P1;giAAR00925 sequence:giAAR00925:::::::0.00: 0.00 MGRLQRFSAFVPLTLSF... ________________________________________ Från: modeller_usage-bounces(a)salilab.org [modeller_usage-bounces(a)salilab.org] för modeller_usage-request(a)salilab.org [modeller_usage-request(a)salilab.org] Skickat: den 23 oktober 2009 08:42 Till: modeller_usage(a)salilab.org Ämne: modeller_usage Digest, Vol 8, Issue 78 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. ERROR ALIGN_CODES (Leonardo Herrera) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Oct 2009 23:42:04 -0700 From: Leonardo Herrera <ldhz04(a)yahoo.com.mx> To: modeller_usage(a)salilab.org Subject: [modeller_usage] ERROR ALIGN_CODES Message-ID: <18c41c7f0910222342g41b9c28eq848322c47110f8d9(a)mail.gmail.com> Content-Type: text/plain; charset="windows-1252" Hi modeller user's I have a problem when I am realising my model with multiple templates, in the step to align the alignment of pdb's versus my sequence I obtain the following problem? Traceback (most recent call last): File "align2d_mult.py", line 14, in <module> aln.append(file='Tc30.ali', align_codes='giAAR00925') File "/usr/lib/python2.6/site-packages/modeller/alignment.py", line 79, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 13) = giAAR00925 I could'nt find an answer to this problem, it already changes the format (fasta to pir ...), and code several times (giAAR00925 to 13... to c30 ...), so please can somebody help with this error message? thanks in advance My script is from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned structure(s): aln = alignment(env) aln.append(file='alineamiento.ali', align_codes='all') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='Tc30.ali', align_codes='giAAR00925') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(output='', max_gap_length=20, gap_function=True, # to use structure-dependent gap penalty alignment_type='PAIRWISE', align_block=aln_block, feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0, gap_penalties_1d=(-450, 0), gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.), similarity_flag=True) aln.write(file='Tc30-mult.ali', alignment_format='PIR') aln.write(file='Tc30-mult.pap', alignment_format='PAP') my Tc30.ali is giAAR00925 524 residues MGRLQRFSAFVPLTLSFISQASAAIGPVTDLTISDADISPDGFTRAAVVMNDQFPGPLIAGNKGDNFQINVI DNLSNSTMLTSTTIHWHGFFQKGTNWADGAAFVNQCPISAGNSFLYDFTATDQAGTFWYHSHLSTQYCDGLR GPMVVYDPDDPHASLYDVDDDSTVITLSDWYHTAARLGARFPAGADSTLINGLGRAAGGDADAALAVFNVTQ GSRYRFRLVSLSCDPNFNFTIQDHNMTIIEVDGVNVEPVTVDSIQIFAGQRYSFVLTADQDIGNYWIQAVPN TGTVTTDGGVNSAILRYDTADPIEPDAADPTSSIPLVETDLVPLENLAAPGDPTVGGVDLAMNLEFDFNGTW FFINGEPFVPPSVPVLLQIMSGAQSAADLLPSGSVYTLPANSTIEISFPMNTTAAPGAPHPFHLHGHTFYVV RSAGSTEYNYVNPPQRDTVSTGTDGDNVTIRFTTNNPGPWFLHCHIDFHLDAGFAIVLSEDTPDAASANTPS SAWDDLCPTYNTDYPDGLGR* and my alineamiento.ali is >P1;1gw0.10wA structureX:1gw0.10w_fit.pdb: 1 :A:+573 :A:::-1.00:-1.00 --EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANW GDTVEVTVINNLV----TNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRAR-QYGTSWYHSHFSA QYGNGVVGTIQING---PASLPYDID--LGVFPITDYYYRAADDLVHFTQN-----NAPPFSDNVLINGTAVNPN TGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAP -DNYWFNVTFGGQAACGG-----SLNPH----PAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSV-- PVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGN------TSYPVSDNIVQVDAVDQWT YWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQ-RFVFDPAVDLARLNGDNPPRRDTTMLPAG---GW LLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL-- ----------------------....wwwwwwwwww* >P1;1gyc.10wA structureX:1gyc.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 AI--------------------------------GPAASLVVANA--PVSPDG-FLRDAIVVNGVFPSPLITGKK GDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIAS-GHSFLYDFHVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPR----------FPLGADATLINGLGRSAS TPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTV -GNYWIRANPN--F---------GTVGFAGGINSAILRYQGAPVAEPTTTQTTS-VIP-LIETNLHPLARMPVPG SPTPGGVDKALNLAFNFNG-----TNFFINNASFTPP-TVPVLLQILSG---AQTAQDLLPAGSVYPLP-AHSTI EITLPATA-LAPGAPHPFHLHGHAFAVVRSAGS----------------T--TYNYNDPIFRDVVSTGTPAAGDN VTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAA--NPVPKAWSDLCPIYDGLSEANQ---------- ----------------------....wwwwwwwwww* >P1;1kya.10wA structureX:1kya.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 GI--------------------------------GPVADLTITNA--AVSPDG-FSRQAVVVNGGTPGPLITGNM GDRFQLNVIDNLTNHTMLKSTSIHWHGFFQKGTNWADGPAFINQCPISS-GHSFLYDFQVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPNDPAADLYDVDNDDTVITLVDWYHVAAKLGPA----------FPLGADATLINGKGRSPS TTTADLSVISVTPGKRYRFRLVSLSCDPNYTFSIDGHNMTIIETDSINTAPLVVDSIQIFAAQRYSFVLEANQAV -DNYWIRANPN--F---------GNVGFTGGINSAILRYDGAAAVEPTTTQTTS-TAP-LNEVNLHPLVATAVPG SPVAGGVDLAINMAFNFNG-----TNFFINGASFTPP-TVPVLLQIISG---AQNAQDLLPSGSVYSLP-SNADI EISFPATA-AAPGAPHPFHLHGHAFAVVRSAGS----------------T--VYNYDNPIFRDVVSTGTPAAGDN VTIRFRTDNPGPWFLHCHIDFHLEAGFAVVFAEDIPDVASA--NPVPQAWSDLCPTYDARDPSDQ---------- ----------------------....wwwwwwwwww* -- MenB Leonardo David Herrera Z??iga POSGRADO EN QU?MICA UAMI Biofisicoqu?mica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674

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