- modeller_usage - salilab.org

residue selection by sequence
by Shyam Saladi 09 Mar '18

09 Mar '18

Hello, It is possible to specify a selection by the sequence of their residues? Usually, I use model.residue_range(), but this can be tedious. Ideally, I'd like to do something like model.residue_sequence('NNPLGTPGTS') to select all occurrences of that sequence. Thanks, Shyam

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Help with rigid body minimization of protein-protein complex
by mromero＠bsc.es 13 Feb '18

13 Feb '18

Hello, I have been testing whether I could use Modeller to minimize a protein-protein complex. As a first test, I've tried to perform a rigid body minimization of the bound structures of receptor and ligand. Even though the starting structure has a Lig-RMSD of 3 A from the native complex structure (i.e., after superimposing the receptor subunits and measuring the CA RMSD between the ligand subunits), the final minimized structure does not get closer to the native complex but goes farther away, with Lig-RMSD of 12 A. I've tried with several near-native conformations and different protein complexes with similar results. The script I am running is the following: from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients, molecular_dynamics, actions env = environ() env.io.atom_files_directory = ['../atom_files'] env.edat.dynamic_sphere = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = "test.pdb" mdl = complete_pdb(env, code) mdl.write(file=code+'.ini') # Select rigid bodies # Receptor rigid body atmsel_a = mdl.chains['A'].atoms r_a = rigid_body(atmsel_a) # Ligand rigid body atmsel_b = mdl.chains['B'].atoms r_b = rigid_body(atmsel_b) # Select all atoms: atmsel = selection(mdl) # Generate the restraints: mdl.restraints.rigid_bodies.append(r_a) mdl.restraints.rigid_bodies.append(r_b) mdl.restraints.make(atmsel, restraint_type='STEREO', spline_on_site=False) mdl.restraints.write(file=code+'.rsr') mpdf = atmsel.energy() # Create optimizer objects and set defaults for all further optimizations cg = conjugate_gradients(output='REPORT') md = molecular_dynamics(output='REPORT') # Open a file to get basic stats on each optimization trcfil = open(code+'.D00000001', 'w') # Run CG on the all-atom selection; write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil)) # Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every # 10 steps during the run, and write stats every 10 steps md.optimize(atmsel, temperature=300, max_iterations=20, actions=[actions.write_structure(10, code+'.D9999%04d.pdb'), actions.trace(10, trcfil)]) # Finish off with some more CG, and write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)]) mpdf = atmsel.energy() mdl.write(file=code+'.B') I have also played with several minimization schemes, with and without MD, but the final minimized model does not get closer to the native complex. Thanks in advance, Miguel http://bsc.es/disclaimer

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How to make better conformational sampling of models using MODELLER?
by Mahesh VELUSAMY 30 Jan '18

30 Jan '18

Hi All, As per the suggestion given in the modeller that changing random seed would helps in producing different models. On this note I have tried to generate 100 models from single template and using different random seeds. It was mainly performed to know how changing random seed influencing on conformational sampling ?. Following the experiment I had observed that there was notable fluctuations on the sidechain orientations. But when I aligned all the models against top model (DOPE SCORE) there was no variations on the backbone conformation and also in terms of RMSD. Following these observations I have a couple of questions for the modeller experts as follows: When modeller says changing random seed helps in finding different models, does it meant for sidechain orientations or backbone? Is it possible to produce models in modeller that will have more variations on the backbone and in terms of RMSD ? Thanking you in advance

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modeller error; " ValueError: too many arguments to unpack"
by Sourav Pal 19 Jan '18

19 Jan '18

I am going to generate a monomer from one single Template (tseq1) by modeller. But there one problem is arised. I have a only one template. According to the basic tutorial of modeller.. I made alignment file like this, (where tseq1 is single template file)from modeller import *env = environ()aln = alignment(env)for (pdb, chain) in (('tseq1', '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)That time it was failed to run by showing the following error"ValueError:too many values to unpack" .can anyone tell me where is the problem? Thank you.Best Regards. Sourav Pal JRF

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Modelling of Homotrimeric protein without biological assembly
by Sourav Pal 17 Jan '18

17 Jan '18

Actually I want to build a homology model of a human homotrimeric protein from a FASTA sequences. After BLAST I got a template which is 91% identical but it is originated from Mouse organism. and it is cryo EM structure.From there, I build a single monomeric chain of that human protein by Homology modelling. But it doesn't contain any biological assembly or asymmetric unit. So that, i am unable to build its trimeric structure. so, can you help me in two sections;1) how to build its homotrimeric structure?2) is there any way to generate the biological assembly coordinates from homology protein?Thanks in advance.Best regards.

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Optimization of an existing loop model
by Claire Marks 17 Jan '18

17 Jan '18

Hi! I would like to use MODELLER to optimize some models that I have generated as part of a loop prediction protocol. The loop conformations were built onto crystal structures downloaded onto the PDB; ideally I only want the loop region to be optimized. I thought the code given on the following web page would be what I should use, however it doesn't seem to do what I want: https://salilab.org/modeller/manual/node36.html This still generates the initial 'straight' conformation that the MODELLER loop modelling algorithm starts from; it doesn't start from the loop conformation in the file I provided. Is anyone able to shed some light on this for me? Claire

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Fw: Builing of homotrimer from a homology structure
by Sourav Pal 16 Jan '18

16 Jan '18

Hello, Actually I want to build a homology model of a human homotrimeric protein from a FASTA sequences. After BLAST I got a template which is 91% identical but it is originated from Mouse organism. And it is the Cryo-EM structure. >From there, I build a single monomeric chain of that human protein by Homology modelling. But it doesn't contain any biological assembly or asymmetric unit. So that, i am unable to build its trimeric structure. so, can you help me in two sections; 1) how to build its homotrimeric structure? 2) is there any way to generate the biological assembly coordinates from homology protein? Thanks in advance. Best regards. Sourav PalSenior Project FellowResearch Group of Dr. Arindam TalukdarCSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, India

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read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file
by Andrea Spinelli 16 Jan '18

16 Jan '18

Hello everybody! I am new to Modeller, so please excuse me if my question seems stupid. I build a model from multiple templates following your tutorial (https://salilab.org/modeller/tutorial/advanced.html) It's working. When I try to develop a module function with scripts, the 'align2d_mult.py' give me the following error: ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 3) = P02489 I can't understand because my sequence.ali file is built in the right way: >P1;P02489 sequence:P02489:::::::0.00: 0.00 MDVTIQHPWFKRTLGPFYPSRLFDQFFGEGLFEYDLLPFLSSTISPYYRQSLFRTVLDSGISEVRSDRDKFVIFLDVKHFSPEDLTVKVQDDFVEIHGKHNERQDDHGYISREFHRRYRLPSNVDQSALSCSLSADGMLTFCGPKIQTGLDATHAERAIPVSREEKPTSAPSS* In attached you can find the python module with the function of script Thank you. Andrea

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mail about an error
by vidhya sankar 02 Jan '18

02 Jan '18

Dear users I am beginner of modeller when i do basic homology modeling i got error as follows read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment MNQVQRSNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWA PDB TVGYLEQKMFAAMVADNQMAMVMLNPKNLKASNGEEELAGQTWYWKVAPVATTQP Match * Alignment residue type 11 (M, MET) does not match pdb residue type 17 (T, THR), for align code 2ret (atom file 2ret), pdb residue number "30", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Even i searched the mailing list i got information but i am not able to understand error . Please is very useful if you point out where i have committed the mistake Thanks in advance with high regardsS.vidhyasnakr

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grid_search and hetatm
by Carlo Camilloni 21 Dec '17

21 Dec '17

Dear Modellers I am fitting a protein with cofactors in a cryo-em density using grid_search. It works but the fitted structure does’t include anymore the HETATM fields with the cofactors. My input looks env = environ() env.io.hetatm = True env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters … den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='SPECIFIC', number_of_steps=1000, angular_step_size=30., temperature=150., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log’) Is this something that is not supported or I am doing something wrong? Best, Carlo _______ Department of Biosciences University of Milano Via Celoria 26 - 20133 Milano, Italy www: sites.unimi.it/camilloni <http://sites.unimi.it/camilloni> www: bioscienze.bio <http://bioscienzebio.unimi.it/>

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