- modeller_usage - salilab.org

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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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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