modeller_usage

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loop_refine.py parallel error
by 刘吉元 30 Jun '11

30 Jun '11

2 1

segfault writing alignment file
by Meesters, Christian 22 Jun '11

22 Jun '11

Hi, I'm using modeller v9.9 in a Linux environment (Ubuntu 11.04) with Python 2.7. When running a script like the build_profile.py from the tutorial, everything works fine, except for the last line: aln.write(file='build_profile.ali', alignment_format='PIR') which results in: openf___224_> Open build_profile.ali Segmentation fault The file is created, but nothing gets written to it. Writing to Python file objects with a simple x = open('test', 'w') x.write('test') x.close() works. So I dare to conclude this is no permissions thing. Although running modeller only via Python, I thought perhaps this is of interest, too: $ ldd mod9.9_x86_64-intel8 linux-vdso.so.1 => (0x00007fff643ff000) libmodeller.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libmodeller.so.5 (0x00007f709af77000) libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f709ac62000) libpython2.3.so.1.0 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libpython2.3.so.1.0 (0x00007f709aa37000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f709a6a3000) libifcore.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libifcore.so.5 (0x00007f709a493000) libsvml.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsvml.so (0x00007f709a308000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f709a104000) libhdf5.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5.so.6 (0x00007f7099c69000) libhdf5_hl.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5_hl.so.6 (0x00007f7099a3d000) libsaxs.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsaxs.so (0x00007f709983c000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f70995ff000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f70993f7000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f70991d9000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f7098fd5000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7098d50000) /lib64/ld-linux-x86-64.so.2 (0x00007f709b52b000) libimf.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libimf.so (0x00007f70989ec000) libintlc.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libintlc.so.5 (0x00007f70988ae000) So, no missing libraries, but perhaps a wrong version? Any ideas on what might trigger this segfault? TIA Christian

2 1

how to download
by Victor 20 Jun '11

20 Jun '11

Hi, How to download Modeller?

2 1

Restrain problem
by flavio seixas 18 Jun '11

18 Jun '11

Hi, I had sucessfull modelled a protein without restrains. However, when I put alpha helix restrains in the script below I face this problem: File "model-restriction-single.py", line 21 rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) ^ IndentationError: unindent does not match any outer indentation level I saw the script too many times and I am not able to see where the problem is. Could anyone help-me? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # Residues 47 through 57 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) # Residues 130 through 140 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('130:', '140:'))) # Residues 182 through 184 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('182:', '184:'))) # Residues 191 through 195 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('191:', '195:'))) a = MyModel(env, alnfile='MODEL-TemplateA.ali', knowns='TemplateA', sequence='MODEL', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 0 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key])

3 2

Fwd: muti template problem
by shikha agarwal 16 Jun '11

16 Jun '11

Hello while performing the modellin using multitemplate I am facing problem . the model-multiple.py , align.ali and generated log files are pasted below . plz help memodel-multiple.py file # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes 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 = ['.', '../atom_files'] a = automodel(env, alnfile = 'align-multiple.ali', # alignment filename knowns = ('2hyd', '3g5u'), # codes of the templates sequence = 'pgp_ref') # 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 modeling C; A multiple alignment in the PIR format; >P1;2hyd structureX:2hyd:1: A:578 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19 ----------------------------------MIKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGVIN ------------NHALTTDEKVHHLTIAIGIALFIFVIVRP-----PIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSA RFYANNQVGQVISRVINDVEQTKDFILTGLMNIWLDCITIFGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILSSFT DKELHAYAKAQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTRALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYL AISGSITVGTLAAFVGYLELLFGPLRRLVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQ YND-NEAPILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLRNQIGLVQQDNILF SDTVKENILLGRPTATDEEV VEAAKMANAHDFIMNLPQGYDTEVGERGVKLSGGQKQRLSIARIFLNNPPILILDEATS ALDLESESIIQEALDVLSKDRTTLIVAHRLSTITHADKIVV IENGHIVETGTHRELIAKQGAYEHLYSIQNL------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- ----------* >P1;3g5u structureX:3g5u:1:A: 1271 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00 MELEEDLKGRADK-NFSKMGKKSKKEKKEKKPAVSVLTMFRYAGWLDRLY MLVGTLAAIIHGVALPLMMLIFGDMTDSF ASVGNVS---KNSTNMSEADK RAMFAKLEEEMTTYAYYYTGIGAGVLIVAYIQVSFWCLAAGRQIHKIRQKFFHAIMNQ EIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQAMATF FGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILS SFTDKELHAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNNNLEEAKRLGIKKAITANISMGAAFLLIYASYALAFWYG TSLVISKEYSIGQVLTVFFSVLIGAFSVGQASPNIEAFANARGAAYEVFKIIDNKPSIDSFSKSGHKPDNIQGNLEFKNI HFSYPSRKEVQILKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEP VLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEA TSALDTESEAVVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFDGGVIVEQGNHDELMREKGIYFKLVMTQTAGNEIEL GNEACKSKDEIDNLDMSSKDSGSSLIRRRSTRKSICGPHDQDRKLSTKEALDEDVPPASFWRILKLNSTEWPYFVVGIFC AIINGGLQPAFSVIFSKVVGVFTNGGPPETQRQNSNLFSLLFLILGIISFITFFLQGFTFGKAGEILTKRLRYMVFKSML RQDVSWFDDPKNTTGALTTRLANDAAQVKGATGSRLAVIFQNIANLGTGIIISLIYGWQLTLLLLAIVPIIAIAGVVEMK MLSGQALKDKKELEGSGKIATEAIENFRTVVSLTREQKFETMYAQSLQIPYRNAMKKAHVFGITFSFTQAMMYFSYAAAF RFGAYLVTQQLMTFENVLLVFSAIVFGAMAVGQVSSFAPDYAKATVSASHIIRIIEKTPEIDSYSTQGLKPNMLEGNVQF SGVVFNYPTRPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVFLDGKEIKQLNVQWLRAQLGIVS QEPILFDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHIL LLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIQNGKVKEHGTHQQLLAQKGIYFSMVSVQAGA KRSYVHHHHHH* >P1;pgp_ref sequence:pgp_ref:1 : :1280 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAIIHGAGLPLMMLVFGEMTDIFA NAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEI GWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIGAAFLLIYASYALAFWYGTTL VLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFS YPSRKEVKILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSA LDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENA ADESKSEIDALEMSSNDSRSSLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKAGEILTKRLRYMVFRSMLRQD VSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNIANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLS GQALKDKKELEGSGKIATEAIENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDSYSTEGLMPNTLEGNVTFGEV VFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEP ILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTKRQ --------* this the log file ate and time of compilation : 2010/04/21 09:52:56 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2010/06/16 12:26:20 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234072 3158.273 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234600 3158.789 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283200 3206.250 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292440 3215.273 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open align-multiple.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303853 3226.419 3.151 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305303 3227.835 3.152 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308203 3230.667 3.155 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3314003 3236.331 3.160 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3325603 3247.659 3.172 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3348803 3270.315 3.194 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3800163 3711.097 3.624 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3802479 3713.358 3.626 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3807623 3718.382 3.631 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3812739 3723.378 3.636 read_al_375E> Unknown residue type,position,sequence: 501 1 -- With Regards: Shikha Agarwal IBI2009009 IIIT-A -- With Regards: Shikha Agarwal IBI2009009 IIIT-A

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 90
by Ashish Runthala 16 Jun '11

16 Jun '11

PDB IDs must be correctly mentioned with their considered chain Identifiers. Good Luck Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Thursday, June 16, 2011 1:35:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 90 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. Re: problem with mac version (Modeller Caretaker) 2. Fwd: muti template problem (shikha agarwal) ---------------------------------------------------------------------- Message: 1 Date: Wed, 08 Jun 2011 10:29:48 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] problem with mac version To: Anthony Couvreux <anthony.couvreux(a)unilim.fr> Cc: modeller_usage(a)salilab.org Message-ID: <4DEFB18C.4070105(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 6/8/11 10:01 AM, Anthony Couvreux wrote: > I have a "segmentation fault" message on my Imac (Mac OS X version 10.5.8). > Even using files that worked successfully on PC. > Does any relation with my Mac configuration? Installedversion of > Python is 2.5.1. See http://salilab.org/modeller/9.9/manual/node10.html Without seeing your input files or any more particulars (e.g. does it crash immediately or partway through the run, what version of Modeller are you using, etc.) it is essentially impossible to help you further. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Thu, 16 Jun 2011 13:35:22 +0530 From: shikha agarwal <shikhaiiitabi(a)gmail.com> Subject: [modeller_usage] Fwd: muti template problem To: modeller_usage(a)salilab.org Message-ID: <BANLkTikpBOx-Hg=3T2CL3G6_oVOybebp5w(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello while performing the modellin using multitemplate I am facing problem . the model-multiple.py , align.ali and generated log files are pasted below . plz help memodel-multiple.py file # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes 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 = ['.', '../atom_files'] a = automodel(env, alnfile = 'align-multiple.ali', # alignment filename knowns = ('2hyd', '3g5u'), # codes of the templates sequence = 'pgp_ref') # 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 modeling C; A multiple alignment in the PIR format; >P1;2hyd structureX:2hyd:1: A:578 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19 ----------------------------------MIKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGVIN ------------NHALTTDEKVHHLTIAIGIALFIFVIVRP-----PIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSA RFYANNQVGQVISRVINDVEQTKDFILTGLMNIWLDCITIFGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILSSFT DKELHAYAKAQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTRALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYL AISGSITVGTLAAFVGYLELLFGPLRRLVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQ YND-NEAPILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLRNQIGLVQQDNILF SDTVKENILLGRPTATDEEV VEAAKMANAHDFIMNLPQGYDTEVGERGVKLSGGQKQRLSIARIFLNNPPILILDEATS ALDLESESIIQEALDVLSKDRTTLIVAHRLSTITHADKIVV IENGHIVETGTHRELIAKQGAYEHLYSIQNL------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- ----------* >P1;3g5u structureX:3g5u:1:A: 1271 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00 MELEEDLKGRADK-NFSKMGKKSKKEKKEKKPAVSVLTMFRYAGWLDRLY MLVGTLAAIIHGVALPLMMLIFGDMTDSF ASVGNVS---KNSTNMSEADK RAMFAKLEEEMTTYAYYYTGIGAGVLIVAYIQVSFWCLAAGRQIHKIRQKFFHAIMNQ EIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQAMATF FGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILS SFTDKELHAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNNNLEEAKRLGIKKAITANISMGAAFLLIYASYALAFWYG TSLVISKEYSIGQVLTVFFSVLIGAFSVGQASPNIEAFANARGAAYEVFKIIDNKPSIDSFSKSGHKPDNIQGNLEFKNI HFSYPSRKEVQILKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEP VLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEA TSALDTESEAVVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFDGGVIVEQGNHDELMREKGIYFKLVMTQTAGNEIEL GNEACKSKDEIDNLDMSSKDSGSSLIRRRSTRKSICGPHDQDRKLSTKEALDEDVPPASFWRILKLNSTEWPYFVVGIFC AIINGGLQPAFSVIFSKVVGVFTNGGPPETQRQNSNLFSLLFLILGIISFITFFLQGFTFGKAGEILTKRLRYMVFKSML RQDVSWFDDPKNTTGALTTRLANDAAQVKGATGSRLAVIFQNIANLGTGIIISLIYGWQLTLLLLAIVPIIAIAGVVEMK MLSGQALKDKKELEGSGKIATEAIENFRTVVSLTREQKFETMYAQSLQIPYRNAMKKAHVFGITFSFTQAMMYFSYAAAF RFGAYLVTQQLMTFENVLLVFSAIVFGAMAVGQVSSFAPDYAKATVSASHIIRIIEKTPEIDSYSTQGLKPNMLEGNVQF SGVVFNYPTRPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVFLDGKEIKQLNVQWLRAQLGIVS QEPILFDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHIL LLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIQNGKVKEHGTHQQLLAQKGIYFSMVSVQAGA KRSYVHHHHHH* >P1;pgp_ref sequence:pgp_ref:1 : :1280 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAIIHGAGLPLMMLVFGEMTDIFA NAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEI GWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIGAAFLLIYASYALAFWYGTTL VLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFS YPSRKEVKILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSA LDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENA ADESKSEIDALEMSSNDSRSSLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKAGEILTKRLRYMVFRSMLRQD VSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNIANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLS GQALKDKKELEGSGKIATEAIENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDSYSTEGLMPNTLEGNVTFGEV VFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEP ILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTKRQ --------* this the log file ate and time of compilation : 2010/04/21 09:52:56 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2010/06/16 12:26:20 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234072 3158.273 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234600 3158.789 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283200 3206.250 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292440 3215.273 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open align-multiple.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303853 3226.419 3.151 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305303 3227.835 3.152 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308203 3230.667 3.155 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3314003 3236.331 3.160 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3325603 3247.659 3.172 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3348803 3270.315 3.194 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3800163 3711.097 3.624 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3802479 3713.358 3.626 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3807623 3718.382 3.631 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3812739 3723.378 3.636 read_al_375E> Unknown residue type,position,sequence: 501 1 -- With Regards: Shikha Agarwal IBI2009009 IIIT-A -- With Regards: Shikha Agarwal IBI2009009 IIIT-A

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problem with mac version
by Anthony Couvreux 08 Jun '11

08 Jun '11

Dear Modeller administrator, I have a "segmentation fault" message on my Imac (Mac OS X version 10.5.8). Even using files that worked successfully on PC. Does any relation with my Mac configuration? Installedversion of Python is 2.5.1. Thank you for your help. -- Anthony Couvreux FACULTE DE MEDECINE 2 Rue DU DOCTEUR MARCLAND 87025 LIMOGES CEDEX

2 1

NADPH
by flavio seixas 25 May '11

25 May '11

Hi, I want to modelate a protein wit NADPH bonded. However, my template has NADH bonded. Here is parte the alignment file I am using with: >structure CCCCCCCCCCCCC4 >sequence BBBBBBBBBBBBB. Were "4" is NADH and "." will repeat NADH. My question is: Which is the align code for NADPH?? If there is no code, how can I replace NADH by NADPH with modeller? Thanks for any help. Flavio Augusto Vicente Seixas Professor Adjunto do Departamento de Bioquímica - DBQ Universidade Estadual de Maringá - UEM Av. Ângelo Moreira da Fonseca, 1800 - Zona 7 87506-370 - UMUARAMA - PR - BRAZIL

2 1

Regarding multiple calls of align2d.py
by Ashish Runthala 24 May '11

24 May '11

Dear Modellers, FIRST and LAST string usage in align2d.py for Initial and final residue number specifier of the concerned template PDB chain generates errors. Why it is so? I should be simply able to alter PDB names in the same align2d.py script without specifying the first and last residue number of the concerned chain. SUGGEST ME THE SOLUTION. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

2 1

Re: [modeller_usage] Loop modelling without changing structure
by Thomas Evangelidis 24 May '11

24 May '11

Yes, this happens quite often. Try to create many homology models without loop modeling (replace MyModel(loopmodel) with class MyModel(automodel), and omit lines starting with a.loop.*) using: a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.very_slow Then chose one model with closed loop ends and use it as the initial conformation to start loop modeling, by following the instructions in my previous email. If the problem persists (probably in case you use multiple templates), paste your alignment here. Usually it's the alignment that requires aditing to make the loops close. Thomas On 24 May 2011 14:08, Matthias Schmidt <matthias.rene.schmidt(a)gmail.com>wrote: > Hi, > > Actually, the modelling works, but the result is not what I hoped for. > Despite having restraints everywhere except for on the loop, Modeller > alters the C-terminus, and it fails to close the loop. > > Hm... Have you seen this before? > > Cheers, > > Matthias > > On Tue, May 24, 2011 at 11:18 AM, Matthias Schmidt > <matthias.rene.schmidt(a)gmail.com> wrote: > > Hi Thomas, > > > > Thank you very much for the hint on the rigid_bodies constraints and > > for your scripts. > > > > It works well. > > > > Best, > > > > Matthias > > > > On Tue, May 24, 2011 at 10:07 AM, Thomas Evangelidis <tevang3(a)gmail.com> > wrote: > >> I'm sorry, I picked the wrong script. Please use the following corrected > >> version: > >> > >> > >> > >>>> class MyModel(loopmodel): > >>>> # This routine picks the residues to be refined by loop modeling > >>>> def select_loop_atoms(self): > >>>> return selection(self.residue_range('310:', '320:'), > >>>> self.residue_range('517:', '523:')) > >>>> > >>>> def special_restraints(self, aln): > >>>> rsr = self.restraints > >>>> # Keep whole model but loop atoms rigid > >>>> wholeSel = selection(self) - self.select_loop_atoms() > >>>> r = rigid_body(wholeSel) > >>>> rsr.rigid_bodies.append(r) > >>> > >>> Then use MyModel in the following way: > >>> > >>>> nv = environ() > >>>> env.io.hetatm = False > >>>> # directories for input atom files > >>>> env.io.atom_files_directory = ["../"] > >>>> a = MyModel(env, > >>>> alnfile = ALIGNMENT, # alignment filename > >>>> knowns = (template1, template2), # codes of the templates > >>>> assess_methods=(assess.DOPEHR,assess.normalized_dope), # > >>>> optionally assess the models on th fly > >>>> sequence=OUTPUT_MODEL_NAME) # code of the > >>>> target > >>>> a.starting_model = 1 # First homology model > >>>> a.ending_model = 1 # Last homology model > >> > >> > >> a.loop.starting_model = 1 # First loop model > >> a.loop.ending_model = 10 # Last loop model > >> a.loop.md_level = refine.very_slow # Loop model > >> refinement level > >>>> > >>>> > >>>> a.library_schedule = autosched.slow > >>>> a.max_var_iterations = 300 > >>>> # Very thorough MD optimization: > >>>> a.md_level = refine.very_slow > >>>> > >>>> a.make() > >>> > >>> > >> > >> In this way you will create a model from your template (if you already > have > >> a model then use it as the template), and then 10 loop decoys by keeping > the > >> rest of the structure rigid. Instead of loopmodel you could use the more > >> accurate dope_loopmodel or even dopehr_loopmodel. You could also start > from > >> an initial structure instead of building one, by using the inimodel > argument > >> within MyModel, i.e. > >> > >> a = MyLoopModel(env, > >> inimodel=initial_structure, > >> loop_assess_methods=assess.DOPEHR, > >> sequence=output_model_name) # code of the > target > >> a.loop.starting_model = 1 # First loop model > >> a.loop.ending_model = 10 # Last loop model > >> a.loop.md_level = refine.very_slow # Loop model refinement > >> level > >> a.make() > >> > >> > >> Whatever way you chose, the key is to define as rigid_body the part of > the > >> structure that you want to be fixed. > >> > >> > >> good luck, > >> Thomas > >> > >> > >>> > >>> > >>> On 24 May 2011 10:25, Matthias Schmidt < > matthias.rene.schmidt(a)gmail.com> > >>> wrote: > >>>> > >>>> Hi, > >>>> > >>>> how can I model a loop without changing the rest of the structure? > >>>> > >>>> Best, > >>>> > >>>> Matthias > >>>> _______________________________________________ > >>>> modeller_usage mailing list > >>>> modeller_usage(a)salilab.org > >>>> https://salilab.org/mailman/listinfo/modeller_usage > >>> > >> > >> > >> > >> Thomas Evangelidis > >> > >> PhD student > >> > >> Biomedical Research Foundation, Academy of Athens > >> > >> 4 Soranou Ephessiou , 115 27 Athens, Greece > >> > >> email: tevang(a)bioacademy.gr > >> > >> tevang3(a)gmail.com > >> > >> website: https://sites.google.com/site/thomasevangelidishomepage/ > >> > >> > > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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modeller_usage