modeller_usage

modeller_usage@salilab.org

3156 discussions

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

3 5

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 still have this error. What else could I do to solve this error. Thank you. mod10.5 align1.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "align1.py", line 56, in ? a.make() # do homology modeling File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 611, in homcsr aln = self.read_alignment() File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 572, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "/usr/lib/modeller10.5/modlib/modeller/alignment.py", line 82, in append allow_alternates) _modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence: % 334 1 -- * Víctor E. Rojas Pérez, Msc.* *Estudiante Doctorado en Biotecnología Traslacional * * Universidad Católica del Maule * *Facultad de Ciencias Agrarias y Forestales* *e-mail: victor.rojas.03(a)alu.ucm.cl <victor.rojas.03(a)alu.ucm.cl>* -- * Víctor E. Rojas Pérez, Msc.* *Estudiante Doctorado en Biotecnología Traslacional * * Universidad Católica del Maule * *Facultad de Ciencias Agrarias y Forestales* *e-mail: victor.rojas.03(a)alu.ucm.cl <victor.rojas.03(a)alu.ucm.cl>*

2 1

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 Amber files and generate RST files from them, but I didn't fully understand how many files I must modify in modeller, or whether I should use the BLK option, but it is not very well documented how to do so. Thanks in advance for any info on this. Pedro

2 1

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.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod10.5' to run them instead. C:\Program Files\Modeller10.5>cd bin C:\Program Files\Modeller10.5\bin>cd Modeller_test C:\Program Files\Modeller10.5\bin\Modeller_test>mod10.5 compare.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 10, in ? aln.malign3d() File "C:\Program Files\Modeller10.5\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 Please, help me.

2 1

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() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod10.5' to run them instead. C:\Program Files\Modeller10.5>cd bin C:\Program Files\Modeller10.5\bin>cd Modeller_test C:\Program Files\Modeller10.5\bin\Modeller_test>mod10.5 compare.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 10, in ? aln.malign3d() File "C:\Program Files\Modeller10.5\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 Please, help me. Thank you very much. Best regards J_FENG

1 0

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 using both chain A and chain B, they have slightly different missing residues in the template but thats fine.For template 2 I cant put them under the same header, modeller doesn't seem to understand that I want to use chain B of template 2 for both chain A and B of my target so I specified it separately - it seems to work fine though with this setup. Unfortunately when I try add HETATM information ".." at the end of my target and template 1 and 2 gaps "--" for template 2 modeller says the whole sequence is out of alignment suddenly. I have specific HETATM=true in my script so it reads that part fine. My alignment looks like this but does not work? Am I missing some obvious? >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--* RegardsKyle

2 3

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 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.

2 1

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 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

3 6

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 . . Jed Goldstone, PhD Biology Department Woods Hole Oceanographic Institution

2 1

_modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables.
by Rana Rehan Khalid 06 May '24

06 May '24

Dear Modeller Users, I am currently attempting to generate various mutant models using the MutantBuilder script available at https://github.com/eved1018/MutantBuilder. I have installed Modeller10.5 for this purpose. However, I am encountering the following issue: python3 MutantBuilder.py -pdb complex.pdb -c B Traceback (most recent call last): File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 372, in <module> main() File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 368, in main model(pdb, mutants, chain, mutant_name, outfolder) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 188, in HomologyModel mutant_pdb = autoModelPDB(pdb, aln ) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 204, in autoModelPDB a.make() File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 638, in homcsr self.mkhomcsr(Selection(self), aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 716, in mkhomcsr self.build_charmm_restraints(atmsel, rsr, aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 678, in build_charmm_restraints rsr.make(atmsel, aln=aln, restraint_type=type+'_dihedral', File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/restraints.py", line 156, in make return func(self.__mdl.modpt, edat.modpt, aln.modpt, io.modpt, _modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables. Could someone please assist me in resolving this problem? Your help would be greatly appreciated. Best Wishes Rehan

2 1

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modeller_usage