modeller_usage

modeller_usage@salilab.org

3151 discussions

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

2 1

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

2 1

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")

2 1

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

1 0

ERROR ALIGN_CODES
by Leonardo Herrera 22 Oct '09

22 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… 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 Zúñiga POSGRADO EN QUÍMICA UAMI Biofisicoquímica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674

1 0

Rebuilding pdball.pir file for mod9v1
by Praveen Raj 22 Oct '09

22 Oct '09

Hi, I would like to know how can we rebuild a new pdball.pir file (for Modeller9v1) from a local copy of PDB files. Please suggest a feasible method to rebuild pdball.pir with the same syntax supported by mod9v1. Thanks in advance for any help Praveen.

2 1

building a model with zn ions
by anu priya 21 Oct '09

21 Oct '09

Hi all, My target protein has two zinc atoms. I aslo obtain the binding sites of these metals in my target sequence. how do i incorporate these zn ions in to my modelled structure? Is it appropriate to include zn ions after modelling or is it neccessary to include it before modelling? Also please give me a procedure to do this like example script files or alignment files or any alternative methods. Thank you. -- G.Anupriya, Research student, National university of singapore.

2 1

ubuntu installation with python 2.6
by Knut J Bjuland 20 Oct '09

20 Oct '09

I have install modeller by following the instruction. An I symlink to /usr/lib/python2.6/site-package. Is there any thing else I might have forgotten to symlink knutb@phenylalanine:~/modeller/basic-example$ python build_profile.py Traceback (most recent call last): File "build_profile.py", line 1, in <module> from modeller import * ImportError: No module named modeller _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

2 1

Parallel modeller
by Hugo Gutiérrez de Teran 13 Oct '09

13 Oct '09

Hi, I want to run parallel job on my Quadcore. I used as a template the script provided in the examples/automodel/model-parallel.py But I get the following error: File "loopmodel.py", line 3, in ? from modeller.parallel import * File "/usr/lib/modeller9v5/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/usr/lib/modeller9v5/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket Thanks for help, Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.teran@usc.es http://web.usc.es/~hugogdt

2 5

Modeling ligands in the binding site
by Qinghua Liao 12 Oct '09

12 Oct '09

Hi modeller users, I want to build a model with a ligand in the binding sites, but I have problems. I read the manual on-line, but I don't find any python script for aligning the sequence to the structure with ligand. I don't know the differences when compared to structure without ligand. Could somebody give me some example of these python script, or give me some suggestion on how to edit the python script which is used to align to structure without ligand? Thanks very much! ALl the best, qinghua

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