- modeller_usage - salilab.org

Reg. Evaluation of multiple template based multi models in one script
by KEDAR SHARMA 14 Jun '18

14 Jun '18

Dear all, i have generated 50 models of my protein using advanced modeling, now i want to evaluate all the models using one script which will give DOPE score, GA341 and molpdf score. Thank you very much. -- -- with regards KEDAR SHARMA PhD Scholar, BSBE Indian Institute of Technology, Guwahati

2 1

Imposing rigid body restraint
by Richard E. Gillilan 05 Jun '18

05 Jun '18

Trying to hold a range of atoms rigid during optimization. I get an error message. Can anyone spot what I’m doing wrong here? Code: class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('138:A','149:A'))) rsr.add(secondary_structure.alpha(self.residue_range('523:B','530:B'))) r1 = rigid_body(self.residue_range('152:A','384:A')) rsr.rigid_bodies.append(rigid_body(r1)) a = MyModel(env, alnfile='KdpD_full_align.ali', knowns=('KdpD_GAF_bent_dimerA','KdpD_GAF_bent_dimerB','4CTI_mod_HAMP-delA','4CTI_mod_HAMP-delB'), sequence='KdpD_GDK_homodimer', assess_methods=(assess.DOPE, # #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() ———— Result: Traceback (most recent call last): File "model-single-restraint.py", line 28, in <module> a.make() File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 112, in make self.homcsr(exit_stage) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 561, in homcsr self.mkhomcsr(selection(self), aln) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 649, in mkhomcsr self.special_restraints(aln) File "model-single-restraint.py", line 15, in special_restraints rsr.rigid_bodies.append(rigid_body(r1)) File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 77, in append self[dim] = obj File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 38, in __setitem__ self._setfunc(ret, val) File "/Library/modeller-9.19/modlib/modeller/rigid_body_list.py", line 24, in _setfunc _modeller.mod_rigid_body_set(mdl.modpt, indx, obj._get_base_atoms(mdl), File "/Library/modeller-9.19/modlib/modeller/rigid_body.py", line 18, in _get_base_atoms return mdl.get_list_atom_indices(self._atoms, None) File "/Library/modeller-9.19/modlib/modeller/coordinates.py", line 298, in get_list_atom_indices (objinds, mdl) = obj.get_atom_indices() AttributeError: 'rigid_body' object has no attribute 'get_atom_indices'

3 2

Modeller 9.20 release
by Modeller Caretaker 05 Jun '18

05 Jun '18

A new version of Modeller, 9.20, 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 8 or 9, there is no need to reregister for Modeller 9.20 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.20 is primarily a bugfix release relative to the last public release (9.19). See the Modeller manual for a full change log: https://salilab.org/modeller/9.20/manual/node40.html If you encounter bugs in Modeller 9.20, please see https://salilab.org/modeller/9.20/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 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

1 0

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

2 1

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

2 2

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)

2 2

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

10 May '18

1 0

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

2 1

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.

2 1

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

2 1