- modeller_usage - salilab.org

strategies for model refinement
by Irene Newhouse 08 Jan '11

08 Jan '11

I'm a relatively new user of modeller & successfully built a fairly nice model of a protein with 258 residues. It forms a homodimer, and has to be modeled as a dimer, because there's a very flexible loop that can easily adopt conformation that prevent dimerization if the 2nd unit isn't present. [I confirmed that by trying it]. Someone on this group suggested the Molprobity server as a way to assess model quality, for which I'm very grateful. He also suggested relaxing the structure with Rosetta, & after epic battles with python setup & my operating system, I got it up & running. Only to learn from the RosettaCommons forum that Rosetta relax doesn't scale well with chain length & isn't useful for proteins with >200 residues. I managed to get the Molprobity score down to a respectable 2.-something using lots & lots of iterations of Schrodinger Prime loop refinement & side chain minimization. It took about a week of setting up a loop, running it, checking to see if it refined, iterating 'til I could move on, etc. So I'm looking for something a bit less hands-on, if possible. Also, Schrodinger is expensive & my boss may not renew the licenses when this lot expires in March. And finally, Molprobity signaled several C-beta issues in my structure, & Schrodinger just doesn't seem to do much about those. Therefore, I'm looking for other suggestions, preferably freeware, for model refinement. I have tried some loop refinement with Modeller itself, but wasn't thrilled with the outcome. This could easily be because I couldn't find sample scripts to copy, or an explanation of how to tweak the parameters if the loop doesn't seem to be refining. If anyone can point me in those directions, I'd be grateful, too. Thanks so much!

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cyclic peptide modeling
by r.yu＠imb.uq.edu.au 05 Jan '11

05 Jan '11

Dear Users, I want to use modeller to model the cyclopeptide. Before sending question here, I checked the mail-list and found other people had asked similar questions. However, when I tried to solve my own problem based on the suggestion, I still could not get my problem resolved. I have attached the script as following: # Homology modeling by the automodel class from modeller.automodel import * # Load standard Modeller classes env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = '/home/rileiyu/model/single/atom' # Disable default NTER and CTER patching env.patch_default=False class mymodel(automodel): def special_patches(self, aln): # Link between residues 22 and 1 to make chain cyclic: self.patch(residue_type='LINK', residue_ids=('22:', '1:')) a = mymodel(env, alnfile = 'single', # alignment filename knowns = 'mii', # codes of the templates sequence = 'cmii',) # code of the target a.make() # do the actual homology modeling But when I started to model my cyclopepetide the problem appeared as: Traceback (most recent call last): File "model.py", line 21, in ? a.make() # do the actual homology modeling File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 427, in homcsr self.make_initial_model(aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 441, in make_initial_model self.generate_method(self, aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/generate.py", line 25, in transfer_xyz mdl.create_topology(aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 659, in create_topology self.special_patches(aln) File "model.py", line 13, in special_patches self.patch(residue_type='LINK', residue_ids=('22:', '1:')) TypeError: patch() got an unexpected keyword argument 'residue_ids' Can anyone here give me more suggestions please? Very appreciated for your help!

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problem in doing difficuly modeling using modeller 9v8
by ranu sharma 27 Dec '10

27 Dec '10

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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Quiero ser tu amigo en Quepasa.com
by Sergio Garay 27 Dec '10

27 Dec '10

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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

2 1

Новое сообщение
by Vovan 12 Dec '10

12 Dec '10

http://samec.org.ua/

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