- modeller_usage - salilab.org

Protein specified in ALIGN_CODES(i) was not found
by Ahmad Abdelzaher 10 May '18

10 May '18

I know this error usually happens when I get the names incorrectly. However, in this case, everything is fine and it seems to run for a little while, then it starts writing stuff to my .ali file and give the below error. readlinef__W> File: alpha_tubulin.pdb, Line: 4611 Modeller will only read the first 80 characters of this line. readlinef__W> File: alpha_tubulin.pdb, Line: 4612 Modeller will only read the first 80 characters of this line. readlinef__W> File: alpha_tubulin.pdb, Line: 4613 Modeller will only read the first 80 characters of this line. readlinef__W> File: alpha_tubulin.pdb, Line: 4614 Modeller will only read the first 80 characters of this line. readlinef__W> File: alpha_tubulin.pdb, Line: 4615 Modeller will only read the first 80 characters of this line. readlinef__W> File: alpha_tubulin.pdb, Line: 4616 No more warnings will be printed for truncated lines in this file. mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -100.0000 Gap extension penalty : 0.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 3.500 3.500 3.500 0.200 4.000 6.500 2.000 0.000 Break-break bonus : 10000.0000 Length of alignment : 441 Score : 258659.2969 read_al_230W> Alignment code alpha_tubulin is present multiple times in the alignment file! Only the first entry will be read. Suggest you remove the duplicate(s) to avoid confusion. read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = alpha_tubulin.pdb Traceback (most recent call last): File "<ipython-input-12-d935bbc074eb>", line 1, in <module> runfile('/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py', wdir='/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller') File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 714, in runfile execfile(filename, namespace) File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 89, in execfile exec(compile(f.read(), filename, 'exec'), namespace) File "/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py", line 35, in <module> a.make() File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 112, in make self.homcsr(exit_stage) File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 535, in homcsr aln = self.read_alignment() File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 502, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/alignment.py", line 80, in append allow_alternates) ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = alpha_tubulin.pdb

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modeller_query
by niki24＠tezu.ernet.in 02 May '18

02 May '18

Dear Sir, I have been trying to model some structures using the modeller. I would like to know the meaning of the B factor for the modeller generated structures. For most of the structures i am getting a higher B value for some regions of my model. Yours faithfully Nikita Bora * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message.

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modeling a chimeric protein
by Ayesha Fatima 23 Apr '18

23 Apr '18

Dear all, I have to model a chimeric protein of two known sequnces. I have gone through the previous archives and have come across the emails of people who have done it. however, I am confused with how to start the first alignment to get the following alignment file >P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb* >P1;chimera sequence:chimera aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb* is this the .ali file to give for alignment. Which script should I use. Kindly help with which is the correct script to use. Thank you Regards Ayesha Fatima QIUP, Ipoh, Perak

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How define restrains between model and template?
by Mario A Bianchet 02 Apr '18

02 Apr '18

Hi, The bend of the modeled three strands long sheet differs too much from the template. Independently that perhaps that have meaning. I want to make closer to the template. It is not clear (or I am missing it ) if is possible restrains between model and template. Thanks in advance Mario -- ========================================================================= Mario A. Bianchet, Ph.D. | bianchet(a)jhmi.edu Assistant Professor of Neurology, | http://abaco.med.jhmi.edu/~bianchet Biophysics & Biophysical Chemistry | 725 N.Wolfe st, WBSB 608B | Baltimore, Maryland, 21205, USA Structural Enzymology | Phones: +1 (443) 591-7583 (cell) & Thermodynamics Group | +1 (410) 614-8221(work) Johns Hopkins School of Medicine | fax: +1 (410) 955-0637 =========================================================================

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Re: [modeller_usage] How define restrains between model and template?
by Mario A Bianchet 28 Mar '18

28 Mar '18

Hi David Thanks. However, my problem is not a different 2ry structure. The well-modeled 3-strand sheet is bend too much compared to the template. I am looking for something like this: # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['CA:77'],at['CA:418']),mean=1.0, stdev=0.5)) Is there a way to select atoms in the template something like at['{structureX/known...}:CA:47'] to restrain the model? Thanks Mario On 3/28/18 12:34 PM, David Gae wrote: > actually I have minor correction. > > modeller also has restraints for sheets as well. > > # for anti-parallel > rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'], > sheet_h_bonds=-5)) > or > > # for parallel > rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'], > # sheet_h_bonds=5)) > Sincerely, > David > >> On Mar 28, 2018, at 9:30 AM, David Gae <ddgae(a)ucdavis.edu >> <mailto:ddgae@ucdavis.edu>> wrote: >> >> Dear Dr. Bianchet, >> >> This may be a possible solution to keep the model similar to the >> template. You can maintain the secondary characteristics using the >> command below. >> For example, >> # beta-strand residue 1-6 should be an beta-strand >> rsr.add(secondary_structure.strand(self.residue_range('1:', '6:'))) >> >> Regards, >> David >> >> >>> On Mar 28, 2018, at 8:35 AM, Mario A Bianchet <bianchet(a)jhmi.edu >>> <mailto:bianchet@jhmi.edu>> wrote: >>> >>> Hi, >>> >>> The bend of the modeled three strands long sheet differs too much >>> from the template. Independently that perhaps that have meaning. I >>> want to make closer to the template. >>> It is not clear (or I am missing it ) if is possible restrains >>> between model and template. >>> >>> Thanks in advance >>> >>> Mario >>> -- >>> ========================================================================= >>> Mario A. Bianchet, Ph.D. |bianchet(a)jhmi.edu >>> Assistant Professor of Neurology, |http://abaco.med.jhmi.edu/~bianchet >>> Biophysics & Biophysical Chemistry | 725 N.Wolfe st, WBSB 608B >>> | Baltimore, Maryland, 21205, USA >>> Structural Enzymology | Phones: +1 (443) 591-7583 (cell) >>> & Thermodynamics Group | +1 (410) 614-8221(work) >>> Johns Hopkins School of Medicine | fax: +1 (410) 955-0637 >>> ========================================================================= >>> _______________________________________________ >>> modeller_usage mailing list >>> modeller_usage(a)salilab.org <mailto:modeller_usage@salilab.org> >>> https://salilab.org/mailman/listinfo/modeller_usage >> >

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How can I change the outputted structure names?
by Ahmad Abdelzaher 21 Mar '18

21 Mar '18

Hello, I'm following this tutorial here: https://salilab.org/modeller/tutorial/basic.html. It's working great, except for not being able to control the names of the outputted structures. Any attempt to rename the alignment codes would of course give errors like "Protein specified in ALIGN_CODES(i) was not found in the alignment file". Is there a way to control the name of the outputted structures? Regards.

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Evaluate protein-peptide complexes using modeller
by SIMON KØNIG 20 Mar '18

20 Mar '18

Dear all It has been pointed out to me that the evaluation method in modeller (molpdf, GA341 and DOPE) are not applicable for models of protein-peptide complexes. Is this the case? If it is, does anybody then have other recommendation for evaluating/assessing models of complexes ? Best regards Simon

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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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