- modeller_usage - salilab.org

Perodic boundary condition?
by Qizan Chen 05 Apr '24

05 Apr '24

Can the Modeller take periodic boundary conditions into account during modeling? I aim to construct a condensed model, but currently, unwarping the protein to the Modeller and then warping it back leads to incorrect overlaps of side chains. I noticed that symmetry constraints can be added, but my original system is already large, and adding additional images causes crashes.

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Error identifying new atomtypes in $RADII_LIB while adding new residue into modeller topology library
by Neeraj Kumar T . 21 Mar '24

21 Mar '24

I've been trying to add a new residue's (ligand) topology and parameters into modeller library to model accurately. I am following the steps in modeller's FAQ #8: https://salilab.org/modeller/FAQ.html#8. After adding the topology into a copy of "top_heav.lib", and parameters into a copy of "par.lib", and also into copies of "radii.lib" and "solv.lib", I still get errors. This is the initial script I used: ------------------ [image: image.png] -------------------- The above script gives error in the 5th command-line as follows: ------------------------------ *ERROR Case-1:* >>> env.libs.parameters.append(file='$(LIB)/radii_edited.lib') read_pa_233E> No keyword before contents. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/parameters.py", line 25, in append return _modeller.mod_parameters_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_pa_233E> No keyword before contents. >>> ------------------------------- Therefore, I deleted command-lines 5&6, and executed the following script. ----------------------------- [image: image.png] ---------------------------------- And executing the above script gave the following error for the 5th command-line: -------------------------------------- *ERROR Case-2:* >>> env.libs.topology.read(file='$(LIB)/top_heav_edited.lib') read_to_681_> topology.submodel read from topology file: 3 read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 23, in read return self.append(file) File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 28, in append return _modeller.mod_topology_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O -------------------------------- This happens inspite of the fact that I have added the radii of new atomtypes into "radii.lib" file itself, and not in the copy "radii_edited.lib", as follows: [image: image.png]

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Modelling based on two templates - one oligomer and one monomer
by hmad3＠cam.ac.uk 19 Mar '24

19 Mar '24

Hello, I am trying to model a multichain protein using 2 templates - the .pdb file of an oligomer (with the same number of chains as the target) and the .pdb file of the AlphaFold structure of one of the monomers making up the target protein. (When I model using only the oligomer as target, the model of the target looks quite "off".) First scenario: * target protein: 5 of the same chain * template protein 1 ("base template"): a homopentamer * template protein 2 ("sub-template" - i.e. the target protein is first modelled based on the first template then modelled based on the 2nd template): the AF predicted structure of one chain of the target protein (the .pdb file has only one chain). Second scenario: * target protein: a heteropentamer - 2 of one chain + 3 of another chain * template protein 1: as in the previous scenario * template protein 2 (+3): AF predicted structures of the two chains making up the target heteropentamer. There are 2 AF folds, one for each monomer, each one with a single chain. How would I format the alignment file? I look forward to your guidance. Kind regards, Amanda

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Alignment to use when I am modelling a heteromer using a homer as template
by hmad3＠cam.ac.uk 18 Mar '24

18 Mar '24

Hello, I am currently modelling a heteromeric protein using a homomeric protein as a template, as follows: - heteromer subunits (target): 2 x aaaaaaaa + bbbbbbbbb - homomer subunits (template): 3 x cccccccccc When aligning the monomer sequences to be used in the .ali file, should I align aaaaaaaa and cccccccccc separately, then bbbbbbbbb and cccccccccc and use the sequences generated in the FASTA file of each alignment in the .ali file -- or should I align all three sequences at once and use the sequences in the FASTA file in the .ali file? (In the first case, there would be two FASTA files and "cccccccccc" would be aligned differently, and both alignments of cccccccccc would be used in the .ali file. In the second case, there would be one FASTA file.) I look forward to your response. Kind regards, Amanda

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I don't want to use one region of a *target* for construction of my model.
by hmad3＠cam.ac.uk 12 Mar '24

12 Mar '24

Hello, I am modelling a pentameric protein based on a template with missing residues, e.g. aaaaabbbbbdddddeeeee (except the original protein sequence has "ccccc" corresponding to a long disordered region between the "b" and "d", but this is not modelled, hence the FASTA of the protein looks like the above, and the .pdb file and 3D model of the protein would show "missing residues" between "b" and "d") The original sequence of the target protein is: fffffggggghhhhhiiiiijjjjj except "iiiii" is a disordered region which aligns with "ccccc" in the template. If I remove "iiiii" from the sequence before aligning with the above template sequence (without the disordered region), "h" and "j" will be interpreted as continuous in the .pdb file of the target generated, affecting the structure of the protein. How would I make PDB interpret a gap between "h" and "j" that aligns with the gap between "b" and "d" in the template? With thanks and kind regards, Amanda

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Modeller 10.5 release
by Modeller Caretaker 23 Jan '24

23 Jan '24

A new version of Modeller, 10.5, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 9 or 10, there is no need to reregister for Modeller 10.5 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.5 is a minor update that adds support for Python 3.12, improves the mmCIF output, and adds initial support for new-style 12-character PDB IDs. If you encounter bugs in Modeller 10.5, please see https://salilab.org/modeller/10.5/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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[modeller] sequence mismatch error
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure. However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

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DNA atoms changed by modeller
by Pedro Guillem 06 Nov '23

06 Nov '23

Hello all, I have a PDB with a small protein-DNA complex... I induce a point mutation in the protein and then save the mutated PDB. The DNA molecule remains untouched. I noticed my original pdb defines the first base (adenine) with 18 atoms - but the output modeller builds 21 atoms. The first 3 atoms are added. I believe the original input is missing the phosphate group. But I want modeller to leave the DNA alone the way it is. Is there a way to set modeller to leave some chains untouched in the output? Thanks in advance Pedro *MODIFIED BY MODELLER* *A* *TOM 1 P DA B 1 11.378 26.105 39.925 1.00 0.00 PATOM 2 OP1 DA B 1 11.702 25.899 40.057 1.00 0.00 OATOM 3 OP2 DA B 1 12.983 26.076 41.112 1.00 0.00 O* ATOM 4 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 5 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C *ORIGINAL* CRYST1 45.400 56.200 130.800 90.00 90.00 90.00 C 2 2 21 ATOM 1 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 2 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C ATOM 3 C4' DA B 1 14.898 24.947 41.083 1.00 26.90 C ATOM 4 O4' DA B 1 14.923 25.240 42.497 1.00 26.42 O ATOM 5 C3' DA B 1 14.466 23.490 40.907 1.00 27.31 C ATOM 6 O3' DA B 1 15.624 22.725 40.560 1.00 29.53 O ATOM 7 C2' DA B 1 13.955 23.125 42.294 1.00 25.13 C ATOM 8 C1' DA B 1 14.747 24.029 43.236 1.00 24.42 C ATOM 9 N9 DA B 1 14.020 24.367 44.474 1.00 21.51 N ATOM 10 C8 DA B 1 14.404 24.071 45.742 1.00 20.32 C ATOM 11 N7 DA B 1 13.590 24.502 46.649 1.00 21.20 N ATOM 12 C5 DA B 1 12.581 25.132 45.948 1.00 20.03 C ATOM 13 C6 DA B 1 11.424 25.786 46.361 1.00 20.34 C ATOM 14 N6 DA B 1 11.075 25.916 47.640 1.00 20.30 N ATOM 15 N1 DA B 1 10.641 26.293 45.396 1.00 21.27 N ATOM 16 C2 DA B 1 10.993 26.155 44.127 1.00 20.67 C ATOM 17 N3 DA B 1 12.054 25.563 43.615 1.00 21.50 N ATOM 18 C4 DA B 1 12.825 25.060 44.609 1.00 21.31 C

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Making a heterotetramer model, while one of the chain is built by using two template
by rpw641＠sund.ku.dk 03 Nov '23

03 Nov '23

Dear Modeller users As the Subject said, I want to make a heterotetramer model, and make one of the chains by using two template. I know how to make heterotetramer model or build a single chain with multitemplate. The problem is that I don't know how to combine these two in my case. Thank you in advance Best Zhucheng

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Missing residues - restrain crystal coordinates
by Isabel Elliott 18 Oct '23

18 Oct '23

Good afternoon, I am trying to model missing residues into my crystal structure following the method on the website: https://salilab.org/modeller/wiki/Missing_residues. I am also trying to restrain the crystal coordinates so that only missing residues move (and the rest of the original crystal coordinates remain the same) during refinement using the select_atoms method. However when I compare my final models produced by my script to my original crystal structure, I find that the side chains of several amino acids three of four amino acids away from the missing residues have been flipped. How can I ensure that only the missing residues are refined and the crystal coordinates remain the same? I am wondering if I’ve missed something important out of my script. See my script below. Many thanks. from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class log.verbose() # Create log file env = Environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env.io.water = True # Only refine/move missing residues - restrain crystal coordinates class MyModel(LoopModel): #picks residues to be refined by loop modelling def select_loop_atoms(self): #refines residue ranges defined simultaneously return Selection(self.residue_range('5:A', '13:A'), self.residue_range('99:B', '105:B'), self.residue_range('251:D', '256:D')) # redefine the special_patches routine to include additional disulfides def special_patches(self,aln): self.patch(residue_type='DISU',residues=(self.residues['26:A'],self.residues['199:C'])) self.patch(residue_type='DISU',residues=(self.residues['29:A'],self.residues['201:C'])) a = MyModel(env, alnfile = 'alignment.ali', # alignment file knowns = 'xxx', # aa sequence of original template - crystal coordinates sequence = 'xxx_fill', # aa sequence of original template with missing residues filled in loop_assess_methods = (assess.DOPE, assess.DOPEHR, assess.GA341)) a.starting_model= 1 # Index of the first model a.ending_model = 1 # Index of the last model a.loop.starting_model = 1 # First loop refined model a.loop.ending_model = 10 # Last loop refined model a.loop.md_level = refine.fast # Loop model refinement level a.make() # Do modelling

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