- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 130
by Ashish Runthala 26 Dec '10

26 Dec '10

What is the length of the target protein, which you are calling a Difficult one. Your aln file is not found. Attach your align2d.py or salign.py respectively, if you are using single or multiple templates for modeling. Also attach your target sequence target.seq file. Good Luck, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, Birla Institute of Technology & Science, Pilani, Rajasthan - 333031 From: ranu sharma <ranusharma09(a)gmail.com> Subject: [modeller_usage] problem in doing difficuly modeling using modeller 9v8 To: modeller_usage(a)salilab.org Message-ID: <AANLkTikhoQUvqSQA1GkKauo9=XctiXy2v27mX-LWrtYZ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello Sir/Madam, Good Afternoon. I am facing problem while doing Difficult modelling for my protein. It is showing the following error. I am attaching the .aln file, my .pdb and model.py file for your reference. Hope to get a reply from you soon. Thanks & Regards. *ERROR:* C:\Program Files\Modeller9v8\examples\ranu_basic\C4H>mod9v8 model.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model.py", line 9, in ? a.make() File "C:\Program Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li ne 98, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li ne 424, in homcsr self.check_alignment(aln) File "C:\Program Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li ne 406, in check_alignment aln.check() File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line 200, in check self.check_structure_structure(io=io) File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: check_a_282E> Unable to read structural information for alignment sequence: 1 2fdvA This command requires structures. -- Ranu Sharma Msc Bioinformatics, Pune University JRF, National Chemical Laboratory, Pune -- Ranu Sharma Msc Bioinformatics, Pune University JRF, National Chemical Laboratory, Pune -- Ranu Sharma Msc Bioinformatics, Pune University JRF, National Chemical Laboratory, Pune

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Re: [modeller_usage] DOPE and sequence/model length (Modeller Caretaker)
by MUSTAFA BUGHIO 26 Dec '10

26 Dec '10

On Sat, Dec 25, 2010 at 11:30 PM, <modeller_usage-request(a)salilab.org>wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: modified amino acids (Modeller Caretaker) > 2. DOPE and sequence/model length (Starr Hazard) > 3. Re: DOPE and sequence/model length (Modeller Caretaker) > 4. problem in doing difficuly modeling using modeller 9v8 > (ranu sharma) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Dec 2010 10:09:27 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] modified amino acids > To: Mike White <mwhite(a)drexelmed.edu> > Cc: ModellerUsage List List <modeller_usage(a)salilab.org> > Message-ID: <4D0A55D7.9050204(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/16/10 6:04 AM, Mike White wrote: > > I am trying to model a small (22 amino acids) peptide with 3 > > disulfide bonds using structures of 6 related peptides with Modeller > > 9.7. The template peptides have 1-3 modified amino acids > > (pyroglutamate, hydroxyproline, amidated C-termini) and the peptide > > to be modeled has an amidated cysteine as the C-terminus. > > Modeller cannot build models containing modified amino acids, nor can it > use structural information from modified amino acids in your templates > (the only exception is MSE, which Modeller treats as identical to MET). > > Your best option in this case is to edit your template PDB file to > convert the modified amino acids to their unmodified equivalents, build > models with regular cysteine, and modify the C-terminus of the > constructed models. > > > I tried setting env.io.hetatm= True to see if that made a difference, > > but then the routine failed with the following track back: > ... > > I'm not sure why env.io.hetatm = 'True' causes this error > > True and 'True' are two different things. True is a Python boolean; > 'True' is a string. Only the first will work here. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Thu, 16 Dec 2010 14:51:44 -0500 > From: Starr Hazard <hazards(a)musc.edu> > Subject: [modeller_usage] DOPE and sequence/model length > To: modeller_usage(a)salilab.org > Message-ID: <4D0A6DD0.2000407(a)musc.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Folks, > > I have modeled some dimers of a large protein and a much shorter partner > (~350aa for X and about 80aa for Y) . There are crystal templates for > such dimers. The best resolution structures have different large and > small proteins. So I have templates with X'Y' and X''Y''. X' and X'' > are homologs as are Y' and Y''. The Y family is quite variable in > length. When homologs from distant organisms ( eg plant, fungi, fish > mammal) are aligned there are gaps compared to the mammalian templates. > > In mammals X' and X'' are in related but distinct clades. If I model a > yeast X protein to each mammalian template can I say that the yeast > protein is better represented by one or the other template based on a > DOPE score? ( the GA341 scores are not helpful since they are always > 1.000 for these models) > > This is several questions I guess. 1) Are DOPE energies normally > distributed? > Could I > statistically compare DOPE scores of models made with one template to > those from another template. > 2) I have > some evidence that longer XY pairs have "better" DOPE scores than > shorter pairs. Is there a statistical way to control for "length"? > 3) I was > just looking at DOPE scores for two models. One with from an alignment > with gaps and the other from an alignment without gaps. > The PDB > model files are different sizes yet the scores are identical. Does DOPE > ignore regions that are not in the template? > > Starr > > > ------------------------------ > > Message: 3 > Date: Mon, 20 Dec 2010 17:01:01 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] DOPE and sequence/model length > To: Starr Hazard <hazards(a)musc.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <4D0FFC4D.2060005(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/16/2010 11:51 AM, Starr Hazard wrote: > > This is several questions I guess. 1) Are DOPE energies normally > > distributed? Could I statistically compare DOPE scores of models made > > with one template to those from another template. > > DOPE is a sum of individual energies over all pairs of atoms in your > final model - it does not include any information from the template or > modeling process. So you can compare DOPE scores for two models of the > same sequence, regardless of their source. > > > 2) I have some evidence that longer XY pairs have "better" DOPE > > scores than shorter pairs. Is there a statistical way to control for > > "length"? > > You can't compare these directly. Use the normalized DOPE score instead, > which *is* corrected for length (it is a z score). > > > 3) I was just looking at DOPE scores for two models. One with from an > > alignment with gaps and the other from an alignment without gaps. > > The PDB model files are different sizes yet the scores are identical. > > Does DOPE ignore regions that are not in the template? > > Yes. See (1) above. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Sun, 26 Dec 2010 13:00:39 +0530 > From: ranu sharma <ranusharma09(a)gmail.com> > Subject: [modeller_usage] problem in doing difficuly modeling using > modeller 9v8 > To: modeller_usage(a)salilab.org > Message-ID: > <AANLkTikhoQUvqSQA1GkKauo9=XctiXy2v27mX-LWrtYZ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Sir/Madam, > > Good Afternoon. I am facing problem while doing Difficult modelling for my > protein. It is showing the following error. > I am attaching the .aln file, my .pdb and model.py file for your reference. > Hope to get a reply from you soon. > > > > > > Thanks & Regards. > > > *ERROR:* > > C:\Program Files\Modeller9v8\examples\ranu_basic\C4H>mod9v8 model.py > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "model.py", line 9, in ? > a.make() > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 98, in make > self.homcsr(exit_stage) > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 424, in homcsr > self.check_alignment(aln) > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 406, in check_alignment > aln.check() > File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line > 200, in > check > self.check_structure_structure(io=io) > File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line > 209, in > check_structure_structure > return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) > _modeller.ModellerError: check_a_282E> Unable to read structural > information > for > alignment sequence: 1 2fdvA This command requires structures. > > > > > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune >

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DOPE and sequence/model length
by Starr Hazard 20 Dec '10

20 Dec '10

Folks, I have modeled some dimers of a large protein and a much shorter partner (~350aa for X and about 80aa for Y) . There are crystal templates for such dimers. The best resolution structures have different large and small proteins. So I have templates with X'Y' and X''Y''. X' and X'' are homologs as are Y' and Y''. The Y family is quite variable in length. When homologs from distant organisms ( eg plant, fungi, fish mammal) are aligned there are gaps compared to the mammalian templates. In mammals X' and X'' are in related but distinct clades. If I model a yeast X protein to each mammalian template can I say that the yeast protein is better represented by one or the other template based on a DOPE score? ( the GA341 scores are not helpful since they are always 1.000 for these models) This is several questions I guess. 1) Are DOPE energies normally distributed? Could I statistically compare DOPE scores of models made with one template to those from another template. 2) I have some evidence that longer XY pairs have "better" DOPE scores than shorter pairs. Is there a statistical way to control for "length"? 3) I was just looking at DOPE scores for two models. One with from an alignment with gaps and the other from an alignment without gaps. The PDB model files are different sizes yet the scores are identical. Does DOPE ignore regions that are not in the template? Starr

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modified amino acids
by Mike White 16 Dec '10

16 Dec '10

Hello I am trying to model a small (22 amino acids) peptide with 3 disulfide bonds using structures of 6 related peptides with Modeller 9.7. The template peptides have 1-3 modified amino acids (pyroglutamate, hydroxyproline, amidated C-termini) and the peptide to be modeled has an amidated cysteine as the C-terminus. Pyroglu is already in the restyp.lib file, and I added HYP as HETATM | HYP | O | | #### | hydroxyproline When I try to align the templates, all of the modified amino acids are missing from the alignments, and since each template has different numbers of modified residues, the reported alignment doesn't even get most of the cysteines aligned. I tried setting env.io.hetatm= True to see if that made a difference, but then the routine failed with the following track back: ____________________________________________________________________ Traceback (most recent call last): File "salignCTX.py", line 21, in ? mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) File "/Library/modeller-9v7/modlib/modeller/model.py", line 72, in __init__ self.read(**vars) File "/Library/modeller-9v7/modlib/modeller/model.py", line 115, in read return _modeller.mod_model_read(self.modpt, io.modpt, File "/Library/modeller-9v7/modlib/modeller/io_data.py", line 56, in __get_modpt self.__atom_files_directory) TypeError: in method 'mod_io_data_set', argument 3 of type 'gboolean' ____________________________________________________________________ I'm not sure why env.io.hetatm = 'True' causes this error, since the routine runs fine under the default condition (env.io.hetatm = 'False') the alignment routine is below (with "env.io.hetatm = 'True' commented out): _________________________________________________________________ from modeller import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files/' # env.io.hetatm = 'True' aln = alignment(env) for (code, chain) in (('1jlo', 'A'), ('1jlp', 'A'), ('1gib', 'A'), ('1tcg', 'A'), ('1r9i','A'),('1q2j','A')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoff=3.5,normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-100.0, 0.0), gap_penalties_3d=(0.0, 3.0), gap_gap_score=0, gap_residue_score=0, dendrogram_file='M_conotoxins.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structures will be # aligned sequentially to the first feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='M_conotoxins.pap', alignment_format='PAP') aln.write(file='M_conotoxins.ali', alignment_format='PIR') aln.salign(rms_cutoff=1.0,normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-100.0, 0.0), gap_penalties_3d=(0.0, 3.0), gap_gap_score=0, gap_residue_score=0, dendrogram_file='M_conotoxins.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY') ____________________________________________________________________ How does one get the modified amino acids to be part of the alignment process? Since the peptides are small, the modified amino acids comprise a significant portion of the total peptide. When one gets to the actual modeling, are these residues also ignored or set to something like the parent amino acid (i.e., proline for HYP)? Thanks! Mike White

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fragment modeling
by SR.Sathya Baarathi 15 Dec '10

15 Dec '10

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Новое сообщение
by Vovan 12 Dec '10

12 Dec '10

http://samec.org.ua/

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refining bad backbone & side chain angles
by Irene Newhouse 08 Dec '10

08 Dec '10

Following an earlier message on the topic of refining a homology model, I just tried a Chimera minimization. The results underwhelm me: Procheck before minimization had 34/576 residues marked with bad phi, psi angles & 10 with bad chi angles. After minimization, there were 40 residues with bad phi, psi angles & 11 with bad chi angles. That's NOT the direction I was looking for! The template structure contained 454 residues, of which only 2 were marked for phi, psi angles by Procheck, and 4 for chi angles. There's only 27% identity, so that's probably part of the issue. Any recommendations? Thanks! Irene Newhouse

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mutant two ore more residues
by Knut J Bjuland 03 Dec '10

03 Dec '10

I have made some modification to the mutant script at the modeller wiki. The change may be seen as patch to the original file. I I whised to change residue 1M and 3P to 1T and E3 in 1B72 is this the way to go. Ca s.mutant be used to select two residues? Knut J --- mutant.py 2010-12-01 09:04:33.004206998 +0100 +++ mutant2.py 2010-12-01 13:09:02.334207000 +0100 @@ -65,7 +65,7 @@ spline_on_site=True) #first argument -modelname, respos, restyp, chain, = sys.argv[1:] +modelname, respos, restyp, chain, respos2, restyp2, chain2 = sys.argv[1:] log.verbose() @@ -98,6 +98,12 @@ #perform the mutate residue operation s.mutate(residue_type=restyp) + + +s1=selection(mdl1.chains[chain2].residues[respos2]) +s1.mutate(residue_type=restyp2) + + #get two copies of the sequence. A modeller trick to get things set up ali.append_model(mdl1, align_codes=modelname) @@ -145,26 +151,30 @@ #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment s = selection(mdl1.chains[chain].residues[respos]) - +s1=selection(mdl1.chains[chain2].residues[respos2]) mdl1.restraints.unpick_all() mdl1.restraints.pick(s) s.energy() +s1.energy() s.randomize_xyz(deviation=4.0) +s1.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(s, sched) +optimize(s1, sched) #feels environment (energy computed on pairs that have at least one member #in the selected) mdl1.env.edat.nonbonded_sel_atoms=1 optimize(s, sched) +optimize(s1, sched) s.energy() - +s1.energy() #give a proper name -mdl1.write(file=modelname+restyp+respos+'.pdb') +mdl1.write(file=modelname+restyp+respos+'_'+respos2+restyp2+'.pdb') #delete the temporary file os.remove(modelname+restyp+respos+'.tmp')

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error using mutate_model.py
by Anna Marabotti 01 Dec '10

01 Dec '10

Hi, I tried to apply the script mutate_model.py to introduce a single point mutation on a protein, and I obtained an error: I'm attaching here the .log file. >From the error message, I see that mutate_model seems to be unable to manage a protein with chain breaks. I can obviously follow the suggestion and relabel the chains of my protein; however, chain breaks are a quite common situation in PDB files, therefore I wonder if there is a way to correct this problem without changing the chain ID as suggested in the log file (which is formally uncorrect since I don't have multiple chains in my protein). Any help will be appreciated. Many thanks in advance and best regards Anna Marabotti __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabotti(a)isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man"

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A better way to do this?
by Stéphane Téletchéa 01 Dec '10

01 Dec '10

Dear users, I'm willing to create a peptide sequence from a fasta sequence, and add a disulfide bridge in it. At the moment, my code "which works" is like this pseudo-code: 1 - create a model object, and model.build('sequence'), I am not applying any time of secondary structure constraint 2 - write this pdb (peptide.pdb) 3 - create a special align where target and template are identical (peptide.ali) 4 - create a new object, Mymodel derived from automodel to add the patch for disulfides 5 - generate models 6 - select the best one (peptide-cys.pdb) I'm only willing to retrieve the "peptide-cys.pdb" file, can I bypass steps 2,3 and act directly on the initial model object created? The implementation of the pseudo-code above is: ##################################################################### # This demonstrates the use of alignment.append_sequence() and # model.build_sequence() to build residue sequences from one-letter codes # http://salilab.org/modeller/manual/node171.html from modeller import * from modeller.automodel import * env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib') # Create a new empty alignment and model: aln = alignment(env) mdl = model(env) mdl.build_sequence('ACAAAAACYAAAA') mdl.write(file='pept.pdb') class MyModel(automodel): def special_patches(self, aln): # The disulfide bridge is taken from the input sequence self.patch(residue_type='DISU', residues=(self.residues['2', self.residues['8'])) a = MyModel(env, alnfile = "tmppiralign.ali", knowns = "pept", sequence = "pept-cys") a.starting_model= 1 a.ending_model = 10 a.make() ##################################################################### tmppiralign.ali is of the form: ##################################################################### >P1;pept structureX:pept:1: :13: :::: ACAAAAACYAAAA* >P1;pept-cys sequence:pept-cys::FIRST:@ END ::::: ACAAAAACYAAAA* ##################################################################### Thanks a lot for corrections, suggestions,.. Stéphane

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