May 2018 - modeller_usage

mutation including fixed new-atom/old-atom distance
by Maria Sola i Vilarrubias 29 May '18

29 May '18

Dear modeller supporters, I want to generate a single site mutation in a dimer and for this, I have successfully run mutate_model.py. However, in the new model, I would like to impose a fixed distance between a nitrogen from the mutated residue and an oxygen from a second residue that belongs to the other subunit. In detail: I want to mutate residue 38 from molA to Arg, and impose that the NE from new Arg38 is at a 2.68 Angstroms distance of molB Glu27 OE1. To impose this I understand I should write: rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['OE1:27:B'], at['NE:38:A']), mean=2.68, stdev=0.1)) But I don't know where to add this in mutate_model.py Could you please help me with this? With best regards, Maria -- Maria Solà Dep. Structural Biology IBMB-CSIC Barcelona Science Park (Helix Building) Baldiri Reixac 15 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.sola(a)ibmb.csic.es

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Reordering chains in template structure
by Ajasja Ljubetič 26 May '18

26 May '18

Hi! I have a template of four single chains, however in the target (single-chain) structure the chain segments are in a different order (as shown in the image). [image: image.png] *Is it possible to somehow specify this correctly in the alignment file?* Currently I reorder the chains in the PDB manually, in order to be able to specify an alignment. If I make four separate entries in the alignment file (one for each chain), then the restraints between the chains are not taken into account and my structure falls apart. Thank you & best regards, Ajasja

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Multiple instance reading the same restraint file
by Ajasja Ljubetič 23 May '18

23 May '18

Dear all, I'm manually parallelizing homology modelling (using the excellent pydoit <http://pydoit.org/>). However, sometimes I get an error of the type Traceback (most recent call last): > File "d:\data\modeller\cocopod\cocopod/make_homology_model.py", line > 138, in <module> > a.make() > File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 116, > in make > self.rd_restraints() > File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 204, > in rd_restraints > self.restraints.append(file=self.csrfile) > File "c:\bin\Modeller\modlib\modeller\restraints.py", line 77, in append > return _modeller.mod_restraints_read(self.__mdl.modpt, fh.file_pointer) > TypeError: dstr_token_E> Could not read an integer at position -1 in input > R 3 1 I'm guessing this happens as one instance of modeller reads an incomplete *.rsr file another instance is writing. (The error does not happen if I run the modelling sequentially, and happens at a random interval otherwise). *My question is: can I rename the *.rsr and *.ini and *.sch files that automodel is using, so **that each instance will have a unique ID?* Thanks & best, Ajasja Ljubetič PS: Currently I'm using automodel with some additional alpha restraints a = AlphaModel(env, alnfile=args.alnfile, knowns=knowns, sequence=sequence, inifile=args.initial_model, assess_methods=[assess.DOPE, assess.GA341, assess.normalized_dope]) a.max_var_iterations = int(args.max_var_iterations) a.md_level = md_opt_dict[args.md_level] a.repeat_optimization = int(args.repeat) a.initial_malign3d = True a.starting_model = int(args.start_index) a.ending_model = int(args.end_index)

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Re: [modeller_usage] modeller_usage Digest, Vol 17, Issue 14
by Jin-Soo Chang 10 May '18

10 May '18

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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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