- modeller_usage - salilab.org

Average the models
by Marco Sette 21 Oct '24

21 Oct '24

Dear all, I have obtained five models of a protein with Modeller and I am analyzing them in relation to the wt. There are of course small deviations, and such differences affect some physical properties. In your opinion, should I analyze the separate models or I can take the average structure? In NMR, people often use an average structure so I wonder if it makes sense in the modelling field. Thanks a lot for your help, Best, Marco -- Dr Marco Sette, PhD. Department of Chemical … [View More]

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model different regions of a protein
by José Xavier 10 Sep '24

10 Sep '24

Dear Modeller users, I'm new here.. so sorry if this is an already answered question. I want to model a protein but the better template doesn't show ~50 aminoácids in its sequence. Is it possible to model the protein based on this template and only the region of ~50 residues based on another template? Thank you for your help Xavier

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Fwd: Error in modeller 10.5
by Victor Eduardo Rojas Pérez 04 Sep '24

04 Sep '24

---------- Forwarded message --------- De: Victor Eduardo Rojas Pérez <victor.rojas.03(a)alu.ucm.cl> Date: mar, 3 sept 2024 a las 13:11 Subject: Error in modeller 10.5 To: Modeller Caretaker <modeller-care(a)salilab.org>, < modeller_usage(a)salilab.org> Dear All, Along with greeting them cordially. I have the following error using modeller 10.5. in linux operating system. I have added the restyp RTN, retinal with % symbol in the restyp.lib file in the modlib folder but I … [View More]

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Using frcmod+off non-standard residue in modeller.
by Pedro Guillem 15 Aug '24

15 Aug '24

Hello, I'm using Modeller to mutate only. I was wondering how hard it would be to mutate any position into a non-standard residue. I have my residues in Amber format (frcmod+off), and I read that I must create the definitions in CHARMM (RST) format, so modeller understands its topology+charges,etc. I also have a PDB file and PRMTOP with the non-standard residue. How hard would it be to make this work in Modeller?. Has anybody done it before? I see that ParmED (for example) can import the … [View More]

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help at second script
by Junyi.FENG＠gustaveroussy.fr 23 Jul '24

23 Jul '24

Hi, While I was running the second script which is called compare.py and is the following: from modeller import * env = Environ() aln = Alignment(env) for (pdb, chain) in (('1jfw', 'A'), ('4ogr', 'D'), ('4or5', 'C'), ('3o6l', 'C'), ('3mi9', 'C'), ('1tbc', 'A'), ('1tiv', 'A')): m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.… [View More]

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help at second script
by FENG Junyi 23 Jul '24

23 Jul '24

Hello, While I was running the second script which is called compare.py and is the following: from modeller import * env = Environ() aln = Alignment(env) for (pdb, chain) in (('1jfw', 'A'), ('4ogr', 'D'), ('4or5', 'C'), ('3o6l', 'C'), ('3mi9', 'C'), ('1tbc', 'A'), ('1tiv', 'A')): m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() … [View More]

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Issues with incorporating ligands in multichain protein
by Kyle- richard Dawson 17 Jun '24

17 Jun '24

Hi there, I am trying to model a multichain protein (homodimer) using 2 templates. I have two issues, Currently my .pir file looks like this >P1;seq1 sequence:seq1:1:A:1224:A:::: xxxx/ xxxx* >P1;template1.pdb structureX:template1.pdb:40:A:651:B:41:B:648:xxxx/xxxx* >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx/-------/ >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:-------/xxxx* Firstly, my template 1 I am … [View More]

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Building multi-chain models
by alina.s123567＠gmail.com 06 Jun '24

06 Jun '24

Good day, I would like to build a GABA A receptor with (two alpha2 subunits chain A, D), (two beta2 subunits chain B, E) and (one gamma subunit chain C). I create an .ali file with template (6HUG) and with target sequences. I have received the error: 'There should be 10 fields separated by colons, : This line actually contains 15 fields.' I don't understand how I should correctly change it, if I have 5 chains. Could you please advise, how I should correctly write this 10 field line. I have … [View More]already read the manual https://salilab.org/modeller/manual/node501.html#alignmentformat, but there is information about 2 chains. I still can not understand how correctly I should write it for 5 chains. The alignment for my template is look like: >P1;6HUG structureX:6HUG:FIRST:A 437:A 473:B 495:C 437:D 473:E:::3.5:-1.00 ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------/ MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK VPEGDVTVILNNLLEGYDNKL---------------RPD----IGVKPTLIHTD-MYVNS IGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADA HWITTPNRMLRIWNDGRVLYTLRLTI----DAECQLQLHNFPMDEHSCPLEFSSYGYPRE EIVYQWKRSSVEV--GDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGY FTIQTYIPC---------------TLIVVLSWVSFWINKD-AVPARTS-LGITTVLTMTT LSTIA----RKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNRKPS------K DKDKKKKNPLLRMFS---FK--------------APTI--------D-I----------- -----------------------------------R------------------------ ---------------PRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFEDCRTGA ---------WRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVS-----YLYLGGSGGSG GSGKTETSQVAPA-/ ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------* Thank you for your help. [View Less]

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Missing Residues at the Start, As Well As in the Middle, of the Sequence of a Chain
by Siddhartha Barua 30 May '24

30 May '24

Dear Modeller Discussion Forum Members, I am trying to repair Chain B in the RCSB PDB 5BS8. 5BS8's structure is that of DNA gyrase (from Mycobacterium tuberculosis). I used the example scripts, for filling in missing residues with Modeller, which were given at the URL https://salilab.org/modeller/wiki/Missing_residues (in Modeller Wiki), as well as the "basic-example" tutorial at the main Modeller website, and a YouTube tutorial video for guidance. *Chain B contains 2 missing residues at the … [View More]start of the sequence associated with the chain in the PDB file- S423 and N424. Thereafter, it contains the sequence "A(425)LVRRK(430)" (with atom records/coordinates) and then a stretch of 6 missing residues- "S(431)ATDIG(436)". *I used the first script given at the abovementioned URL to generate a sequence file extracted from the PDB. *I then used the following as my alignment file (using the NCBI RefSeq (NP_214519.2) for Mycobacterium tuberculosis gyrB (DNA Gyrase subunit B):* >P1;5bs8 structure:5bs8.pdb:FIRST:B:LAST:B:DNA Gyrase::: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALVRRK------GLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV* >P1;5bs8B_fill sequence::::::::: MAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV* *I used the following as the script to run AutoModel to model only the selected residues:* 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('431:B', '436:B')) a = MyModel(env, alnfile = '5bs8_B-alignment.ali', knowns = '5bs8', sequence = '5bs8B_fill') a.starting_model= 1 a.ending_model = 1 *This then raised the following error:* return Selection(self.residue_range('431:B', '436:B')) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 385, in residue_range start = self.residues[start]._num ~~~~~~~~~~~~~^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 302, in __getitem__ ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\util\modutil.py", line 24, in handle_seq_indx int_indx = lookup_func(*args) ^^^^^^^^^^^^^^^^^^ File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 379, in _indxres self._report_bad_index(indx, suffix, "residue", 0) File "C:\Program Files (x86)\Modeller10.5\modlib\modeller\coordinates.py", line 372, in _report_bad_index raise KeyError("No such %s: %s" % (indxtyp, indx)) *KeyError: 'No such residue: 431:B'* Next, I tried to run it again after deleting the 424 "-"s that preceded the sequence in the structure-associated sequence portion of the alignment file (>P1;5bs8 structure:5bs8.pdb:FIRST:B:LAST:B:DNA Gyrase:::) and replacing them with 2 "-"s for S423 and N424 and the again, without these 2 preceding "-"s. Both times, I then got the same error: (...... *KeyError: 'No such residue: 431:B'*) *Please advise me on how to fill in missing residues for a chain that (a) has coordinates only for a middle portion/domain of the entire possible sequence (for the full-length protein) (because only the middle portion/domain was crystallised and subjected to X-ray crystallography, say) and (b) has missing residues at the start of this chain (due to high B-factors, say) with respect to the sequence that is associated with the solved structure of the chain in question (as can be seen in PDB viewer softwares such as UCSF Chimera) (e.g.: chain B of RCSB PDB 5BS8).* Thanks, and regards, Siddhartha A. Barua, Ph.D. -- Siddhartha A. Barua, Ph.D. Mb.: +91 7777093994 [View Less]

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coarse parallelization
by Jed Goldstone 16 May '24

16 May '24

I would like to use coarse-grained parallelization with automodel (through slurm) to create (say) 100 models. As Modeller is deterministic, even if I start a job array with different model numbers, each separate job creates the same models. So, for example, if I start job using 4 different python scrips with model ids 0-24, 25-49,50-74, and 75-99, I will get 4 sets of identical models. How can I turn off this deterministic behavior? With thanks, Jed . … [View More]

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