- modeller_usage - salilab.org

Modeller 10.7 release
by Modeller Caretaker 29 May '25

29 May '25

A new version of Modeller, 10.7, 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 10.7 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.7 is a minor update that improves mmCIF output, adds read support for the BinaryCIF format, better handles the new 5-character PDB residue names, and includes a number of bug fixes. If you encounter bugs in Modeller 10.7, please see https://salilab.org/modeller/10.7/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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Specification of restraints
by Fred Pontes 23 May '25

23 May '25

Hi I'm trying to apply a restraint to keep fixed the CA of a specific residue using a Gaussian form. This mathematical form of restraints accept four arguments: forms.Gaussian(group, feature, mean, stdev) mean and stdev are defined by me according to my system. In the `feature` I could use features.ZCoordinate(*atom_ids). But I`m struggling with the group argument. I think the group is a physical restraints type and I have defined the type `z_coord_type', but I always get an error from MODELLER/10.4. * rsr.add(forms.Gaussian(group=physical.z_coordinate,AttributeError: 'module' object has no attribute 'z_coordinate'* Am I doing this right? Below I include my script file. Thank you in advance. *from modeller import *from modeller.automodel import *from modeller.physical import PhysicalTypez_coord_type = PhysicalType(99, 'z_coordinate')import syslog.verbose()env = Environ()class MyModel(AutoModel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.Gaussian(group=physical.z_coordinate, feature=features.ZCoordinate(at['CA:25:A']), mean=193.8, stdev=0.1)) a = MyModel(env, alnfile='multi-co.ali', knowns=('HPI1_fit'), sequence='multi', assess_methods=(assess.DOPE,assess.GA341))a.starting_model = 1a.ending_model = 10a.make()* -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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restraint distance between template and model
by Fred Pontes 22 May '25

22 May '25

Hi! I asked MODELLER to create a protein model using two templates. I think, my model is quite good, but I see a place to improve in relation to the relative position between some helices. In the template, the helices are close to each other and have a shift in the z-coordinates, but it's not appear in my model. How can I apply a restraint between template and model, in order to have the same relative position between the helices? I tried to draw a scheme below, in order to be more clear about what I'm speaking: Z-axis Relative position that I have in model Relative position that I want and see in template ^ H H H | H H H H | H H H H | H H H H H Kind regards, Fred -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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(no subject)
by Fred Pontes 14 Apr '25

14 Apr '25

Hi! I'm using MODELLER to build a homology model of my protein. In my first try, I create a model without any restraint, and then I compared the secondary structure of this model (Using STRIDE and VMD) with the secondary structure predict by PSIPRED webserver. For the first 26 residues, I have these predictions: PSIPRED: CHHHHHHHHHHHHHHHHHHHHHHHHC Homology model: CCCCCCCCCCCCHHHHHHHHHHHHHC My idea is restraint the region where the predictions are coincidences (13:A to 26:A) and applying restraints to force an alpha Helix structure between residues 3 and 11. I didn't include the residues 2 and 12 in order to give some flexibility to MODELLER to connect the restraint to the remainder of the protein (see below). from modeller import * from modeller.automodel import * import sys log.verbose() env = environ() class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('13:A', '26:A')) def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Define an alpha helix rsr.add(secondary_structure.alpha(self.residue_range('3:A', '11:A'))) But, when I look this region on VMD, I don't have a Helix between residues 2 to 12. I don't know, what I'm doing wrong. Is a better approach to restraint as Helix from 2 to 26? Should I keep some regions without optimization during the restraint protocol? Thank in advance, Fred -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)
by Fred Pontes 01 Apr '25

01 Apr '25

Hi! Sorry for the very basic question, but again I'm facing issues with MODELLER. When I run MODELLER I got the following error: "*_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 6KG7.pdb*" But my structure file is present in my directory: *(base) [medfpo@uol-pc-301925 hPIEZO2_structure]$ ls -l 6KG7.pdb -rw-r--r--. 1 medfpo Domain Users 1177728 Mar 31 13:25 6KG7.pdb* I don't have any idea what's the problem. I didn't misspell any name and the structure file is present. I included one line: *env.io.atom_files_directory = ['.'], *but It didn't change the output error. I included below my script file and alignment file. Thank you in advance. This is my script below: *from modeller import *from modeller.automodel import *import syslog.verbose()env = environ()aln = alignment(env)aln.append(file='align.pir', align_codes=('target', 'template1'))# directories for input atom filesenv.io.atom_files_directory = ['.']* *a = automodel(env, alnfile = 'align.pir', # alignment filename knowns = ('6KG7.pdb'), # codes of the templates sequence = 'target', assess_methods = (assess.DOPE, assess.GA341))a.starting_model = 1 a.ending_model = 5 a.make()# RANK MODELS ACCORDING DOPE score # Get a list of all successfully built models from a.outputs ok_models = [x for x in a.outputs if x['failure'] is None]# Rank the models by DOPE score key = 'DOPE score'if sys.version_info[:2] == (2,3): # Python 2.3's sort doesn't have a key argument ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key])# Get top model m = ok_models[0]print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key]))* and the first 5 lines of my alignment file: ( *base) [medfpo@uol-pc-301925 hPIEZO2_structure]$ head -5 align.pir >P1;template1structure:6KG7.pdb:8:A:2822:A:::-1.00:-1.00-------GLIFRLLLPICLAVACAFRYNGLSFVYLIYLLLIPLFSEPTKATMQGHTGRLLQSLCITSLSFLLLHIIFHI------------------------------------------VFVPDIGMFIASLTIWLVCRT----------------------------------------------------------LRRFASVASKLKEFIGNMITTAGKV* -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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(no subject)
by Fred Pontes 27 Mar '25

27 Mar '25

Hi everyone, I'm a beginner in using MODELLER and I need help to fix my files in my modelling. I'm trying to build a homology model using two templates. I'd like to select different regions of each template to build my model. I attached the script below, In my alignment.pir file I include the sequence of my template in the following way: >P1;template1 structureX:protA.pdb:8:A:2822:A:::-1.00:-1.00 --------------------------------------------------------------------------- ... >P1;template2 structureX:protB.pdb:1:A:2521:A:::-1.00:-1.00 MEPHVLGAVLYWLLLPCALLAACLLRFSGLSLVYLLFLLLLPW ... I replace the amino acid symbol for '-' when they are present in a region that I don't want to use as a template. I didn't modify my pdb files. All residues are present. When I run my job, MODELLER starts to create the target, but always stops at an error related to structure files. Has anyone tried the same thing that I'm trying? I'm using version 10.4 Thank you in advance. from modeller import * from modeller.automodel import * log.verbose() env = Environ() aln = Alignment(env) aln.append(file='alignment.pir', align_codes=('target', 'template1', 'template2')) #class MyModel(AutoModel): # def select_atoms(self): # Select residues 1234 to 2822 from template1, mPiezo2 and 1 to 1200 from template 2 - hPIEZO1 # return selection(self.residue_range('1234:', '2822:'), # self.residue_range('1:', '1200:')) a = AutoModel(env, alnfile='alignment.pir', knowns=('template1', 'template2'), sequence='target', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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what is non-bonded restraints in modeller molpdf
by Li Xue 17 Feb '25

17 Feb '25

Hello all, I am trying to understand the components of modeller molpdf. Does anyone know what the non-bonded restraints are, since modeller by default does not calculate L-J nor electrostatics? Best, Li

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how to calculate energy using modeller
by Li Xue 21 Jan '25

21 Jan '25

Dear Modeller Team, I am currently looking for a quick method for calculating the energy of protein structures. I understand that Modeller utilizes a simplified version of the CHARMM force field, which suits my needs, as I’m looking for a fast and approximate energy calculation. I would like to print out each energy term, but with the current code I’m using, the Lennard-Jones and Coulomb terms are returning zero. Could you please advise on how to resolve this issue? The code that I used: from modeller import * from modeller.scripts import complete_pdb # Initialize MODELLER environment (use Environ instead of environ) env = Environ() # Load topology and parameter libraries env.libs.topology.read(file='$(LIB)/top_heav.lib') # Heavy atom topology env.libs.parameters.read(file='$(LIB)/par.lib') # Parameter library # Read in the protein structure mdl = complete_pdb(env, '3VXU.pdb') # Calculate energy mdl.energy() # Energy calculations are complete print("\nEnergy calculation completed.") --- Thank you for your help. Best, Li

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Reconstruction of CA position only files with all-atom template
by jingkaizeng 13 Nov '24

13 Nov '24

Hi all, Here is my task: I have some CA position only files of a protein of interested that underlying some important biological pathways. We also have the protein full Cryo-EM structures (pdb:8io4, the exact same protein as well as sequence as the CA only files). Then I would like to fill the keep the CA position only files' CA position (don't move at all) then reconstruct the detail like side chain/secondary structure information from template. So this task is not homology modeling but reconstruction. After getting the reconstructed files, I would like to use these into MD simulations. I searched from previous mail list, and I found one did this task but not based on template. https://www.salilab.org/archives/modeller_usage/2008/msg00285.html I tried with " env = Environ() # Load the CA-only seed model seed_model = Model(env, file=seed_file) # Load the template structure (with full atomistic detail) template_model = Model(env, file=template_file) # Create an alignment between the seed and itself (1:1 alignment) aln = Alignment(env) aln.append_model(seed_model, align_codes='seed') aln.append_model(seed_model, align_codes='seed') # Write the alignment for debugging purposes aln.write(file='alignment.ali', alignment_format='PIR') # Define a custom model class to fix the Cα positions class MyModel(automodel): def select_atoms(self): # Select all atoms except the Cα atoms to allow refinement of everything but Cα s = selection(self) return s - s.only_atom_types('CA') # Set up environment for refinement env.edat.nonbonded_sel_atoms = 2 # Disable interactions between selected and unselected atoms a = MyModel(env, alnfile = aln, # Alignment file created earlier knowns = 'seed', # Seed model (CA-only) sequence = 'seed') # Target is also the seed (1:1 alignment) a.starting_model = 1 a.ending_model = 1 a.make() " But this code didn't use the side chain atom from the Cryo-EM structure, and just use CA position to reconstruct the detail. It seems the reconstruction by this code is not reliable enough that cause infinite energy error in MD simulation, it may indicate some overlap or incorrect side-chain orientations, or improper hydrogen placements. Therefore, I would need to try to reconstruct with the side chain information from template Cryo-EM structure's pdb. I tried some methods that use the template Cryo-EM structure, but it seems we just do the homology modeling but NOT reconstruction. The production files we get is almost same as the template without make use of the CA position from CA only files. The code I used like : " # Load the CA-only seed model seed_model = Model(env, file=seed_file) # Load the template structure (with full atomistic detail) template_model = Model(env, file=template_file) # Create an alignment between the seed and the template aln = Alignment(env) aln.append_model(template_model, align_codes='template') aln.append_model(seed_model, align_codes='seed') # Perform the alignment aln.align() # Now defining a custom AutoModel class to apply Cα restraints class MyModel(AutoModel): def special_restraints(self, aln): # Restrain all Cα atoms based on the seed model rsr = self.restraints atmsel = selection(self).only_atom_types('CA') # Apply restraints to the selected Cα atoms for atom in atmsel: rsr.add(forms.Gaussian(group=physical.xy_distance, feature=features.Distance(atom, atom), mean=0.0, # No change in CA positions stdev=0.01)) # Instantiate the custom model class a = MyModel(env, alnfile=aln, knowns='template', sequence='seed') a.starting_model = 1 a.ending_model = 1 a.make() " I think this task can be done since I found a paper (https://doi.org/10.7554/eLife.68369) that do the similar task, they claim to use Modeller to perform this: "First, side chain atoms from the template X-ray structure (PDB ID 4HFI) were added to each model, followed by a cycle of refinement with all Ca atoms restrained. Restraints on Ca atoms were then substituted with restraints on backbone hydrogen bonds, taken from helix and sheet annotations in the template PDB file, for another cycle of refinement to ensure proper secondary structure." Can anyone give some suggestions about this reconstruction task? Thanks. Best, Jingkai

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Missing residues modeling in Modeller
by bbmpresi＠gmail.com 04 Nov '24

04 Nov '24

Dear all, I am trying to model the missing residues in a beta barrel shaped protein that contains 12 missing residues in the original pdb. As instructed for the 1qg8 tutorial, I also first obtained the full amino acid sequence of the protein using: from modeller import * # Get the sequence of the 1qg8 PDB file, and write to an alignment file code = 'pdbid' e = Environ() m = Model(e, file=code) aln = Alignment(e) aln.append_model(m, align_codes=code) aln.write(file=code+'.seq') and I am obtaining an output file named pdbid.seq The actual protein sequence contains 324 amino acid residues and 12 residues are missing in the pdbid.pdb file This is the alignment.ali file I am preparing for missing residue addition: >P1;pdbid structureX:pdbid:1:A:+312:A:MOL_ID 1; ASDQRGYKP------------GGHVGTSVEYEDKVTRGFNNTDKKEKTITNEVFNFFYNNPQWNFMGFYSFKIENREQKEPGYYENEDGIKQLFSLNKGHDLGNGWATGLIYELEYTRSKVYSPDVSGLRKNLAEHSIRPYLTYWNNDYNMGFYSNLEYLLSKEDRNAWGKRQEQGYSALFKPYKRFGNWEVGVEFYYQIKTNDEKQPDGTINEKSDFNERYIEPIVQYSFDDAGTLYTRVRVGKNETKNTDRSGGGNAGINYFKDIRKATVGYEQSIGESWVAKAEYEYANEVEKKSRLSGWEARNKSELTQHTFYAQALYRF* >P1;pdb_fill sequence::::::::: ASDQRGYKPEDVAFDESFFSFGGHVGTSVEYEDKVTRGFNNTDKKEKTITNEVFNFFYNNPQWNFMGFYSFKIENREQKEPGYYENEDGIKQLFSLNKGHDLGNGWATGLIYELEYTRSKVYSPDVSGLRKNLAEHSIRPYLTYWNNDYNMGFYSNLEYLLSKEDRNAWGKRQEQGYSALFKPYKRFGNWEVGVEFYYQIKTNDEKQPDGTINEKSDFNERYIEPIVQYSFDDAGTLYTRVRVGKNETKNTDRSGGGNAGINYFKDIRKATVGYEQSIGESWVAKAEYEYANEVEKKSRLSGWEARNKSELTQHTFYAQALYRF* But in the template I get residue number written as 312 instead of 324, I directly copied the entry from the pdbid.seq file that was provided by Modeller at the first step that I explained at the beginning. Due to 12 missing residues Modeller is reporting 312 residues in the second line of the alignment.ali file: structureX:pdbid:1:A:+312:A:MOL_ID 1; However, I checked other examples on Modeller tutorial and it seems in some examples the total residue numbers (including the missing residue numbers) are written in the template section for the alignment.ali file, so I could have used structureX:pdbid:1:A:+324:A:MOL_ID 1; writing 324 as total number of residues for the template; so my question is that does it matter if write structureX:pdbid:1:A:+312:A:MOL_ID 1; or structureX:pdbid:1:A:+324:A:MOL_ID 1; I generated a new pdb with all missing residues modelled by Modeller using: 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('10:A', '21:A')) #a = MyModel(env, alnfile = 'alignment.ali', # knowns = 'pdbid', sequence = 'pdbid_fill') a = AutoModel(env, alnfile = 'alignment.ali', knowns = 'pdbid', sequence = 'pdbid_fill') a.starting_model= 1 a.ending_model = 5 a.make() I checked that using structureX:pdbid:1:A:+312:A:MOL_ID 1; or structureX:pdbid:1:A:+324:A:MOL_ID 1; in the second line of alignment.ali for the template, I am obtaining a very similar or more or less identical modeled structure. Can anybody tell me if the number of residues written in the second line of alignment.ali file for template pdb matters or not? Or only the template sequence and the gaps really matter? Any help would be much appreciated, thank you

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