- modeller_usage - salilab.org

Ab-initio loop modelling vs. homology loop modelling
by Karolina Markowska 19 Feb '15

19 Feb '15

Dear Modeller-Usage group, I have a problem with my structure. It is lacking 9 amino acids from a loop next to its active center. I've tried to refill it using the loopmodel class script from this tutorial: http://salilab.org/modeller/wiki/Missing%20residues. My script looks like this: # Ab-initio modeling by the loopmodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = 'sEH_AN_A.ali', knowns = 'sEH_AN_A', sequence = 'sEH_AN_A_fill', assess_methods=(assess.DOPE, assess.GA341), loop_assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341)) a.starting_model= 1 a.ending_model = 10 a.loop.starting_model = 1 a.loop.ending_model = 10 a.loop.md_level = refine.fast a.make() I've also find a homologous structure with a complete amino acid sequence but its sequence has only 34% identity with my structure. So I just cut the loop from the homologous and use it as a template. I think that the loop from my structure will be similar to the loop from the homologous structure. My second script looks like that # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'sEH_AN-homolog.ali', knowns = ('homologue', 'sEH_AN_A'), sequence = 'sEH_AN_A_fill', assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341)) a.starting_model= 1 a.ending_model = 100 a.make() Then I compared all the models I've build by Z-score (normalized.DOPE) value and by calculating the RMSD of the created models and homologous structure. The RMSD is very high (1,55 to even 5,48) so I think the models are not so good. Which method will give me more accurate and native-like models? Best regards, Karolina Markowska Silesian University of Technology

1 0

Modelling N and C terminal regions
by Anjela Manandhar 17 Feb '15

17 Feb '15

Hello, I need to model N and C terminal residues. For N terminal it is only 1 residue, whereas for C terminal it is 12 residues. Can I use Loop Refinement for this? Thank you. Anjela Manandhar

2 1

Building a model from Fasta file
by Mouses Stamboulian 13 Feb '15

13 Feb '15

?Dear Ben, I'm trying to run this script. import time from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb #log.level(output=1, notes=1, warnings=1, errors=1, memory=0) log.verbose() env = environ() env.io.atom_files_directory = ['../atom_files'] aln = alignment(env) aln.append(file='5fd1_1fdx_sequence.fasta', align_codes=('5fd1', '1fdx'), alignment_format='FASTA') #aln.append(file='alignment.ali', align_codes=('5fd1', '1fdx')) aln.align() aln.write(file='5fd1_1fdx_output.fasta', alignment_format='FASTA') #aln.write(file='alignment_output.ali') #aln.check() a = automodel(env, alnfile = '5fd1_1fdx_output.fasta', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # code of the target a.starting_model= 10 # index of the first model a.ending_model = 10 # index of the last model a.very_fast() # prepare for extremely fast optimization start_time = time.time() a.make() print("duration for model building is: ", time.time()-start_time)?baci basically I'm taking as input from 5fd1_1fdx_sequence.fasta? file (please find attached) two input protein sequences in FASTA format, and then aligning them with the aln.align() function and writing the output in 5fd1_1fdx_output.fasta then eventually use it to build a model using the automodel function. whenever I call the model.make() function I'm getting this error. Traceback (most recent call last): File "/home/mossig/anaconda/scripts/modeller/automodel/align_fasta.py", line 43, in <module> a.make() File "/usr/lib/modeller9.14/modlib/modeller/automodel/automodel.py", line 110, in make self.homcsr(exit_stage) File "/usr/lib/modeller9.14/modlib/modeller/automodel/automodel.py", line 475, in homcsr aln = self.read_alignment() File "/usr/lib/modeller9.14/modlib/modeller/automodel/automodel.py", line 465, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "/usr/lib/modeller9.14/modlib/modeller/alignment.py", line 79, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 5fd1 ?Can't I build a model from a pairwise fasta alignment? Thank you.

2 1

error: Py_InitModule4_64
by meier＠lmb.uni-muenchen.de 10 Feb '15

10 Feb '15

Hi, I have installed Modeller 9.13 (downloaded http://salilab.org/modeller/9.13/modeller-9.13.tar.gz and executed the Install file). Next, I created a shared library for a user defined constraint as follows: gcc -shared -Wall -fPIC .../bin/modeller9.13/bin/mod9.13 --cflags --libs` `pkg-config --cflags glib-2.0` -I/usr/include/pythonXXX my_rsr.c my_rsr_wrap.c -o _my_rsr.so -lm where XXX stands for different python versions I tried (e.g. 2.5,2.6,2.7) When executing my python script via: ...bin/modeller9.13/bin/mod9.13 my_script.py or ...bin/modeller9.13/bin/modpy.sh pythonXXX my_script.py I always get the error: ImportError: .../bin/modeller9.13/modlib/modeller/_my_rsr.so: undefined symbol: Py_InitModule4_64 I tried to set the python path, but it didn't help. How can I fix this?

3 4

Not refining the CAs of certain residues
by Edelmiro Moman 04 Feb '15

04 Feb '15

Hello, I would like to build protein models in which the CA coordinates of certain residues are identical to those of the (single) template. If I have understood it correctly, the following should do precisely that: class MyModel(automodel): def select_atoms(self): # Refine all atoms except the CAs of residues20-40 and 70-80 : return selection(self) - selection(self.residue_range('20', '40')).only_atom_types('CA') return selection(self) - selection(self.residue_range('70', '80')).only_atom_types('CA') Where the residue numbers correspond to those of the model. Is this correct? Or, if it makes more sense restricting the full backbone of the selected residues, would the following work? class MyModel(automodel): def select_atoms(self): # Refine all atoms except the backbone atoms of residue 20-40 and 70-80: return selection(self) - selection(self.residue_range('20', '40')).only_mainchain() return selection(self) - selection(self.residue_range('70', '80')).only_mainchain() Best regards, Miro -- Edelmiro Moman, PhD ProSciens, computer-aided drug design 2-4 rue du Palais de Justice L-1841 Luxembourg Phone : +352 2728-2588 E-mail : moman(a)prosciens.com http://prosciens.com

3 11

Modeller API
by Mouses Stamboulian 04 Feb '15

04 Feb '15

?Hi, I'm a student at the Lebanese American University and I was wondering if there is an API for Modeller. I want to use modeller in my java code. am I able to call modeller methods through Java? for instance feed the program with two alignments and give a command in my java code to model the 3D strcutre. Thank you.

2 1

Fwd: Request for you Assistance - Molecular modeling
by Swetha Kumari 12 Jan '15

12 Jan '15

---------- Forwarded message ---------- From: Swetha Kumari <swethakumari.k(a)gmail.com> Date: 12 January 2015 at 14:10 Subject: Request for you Assistance - Molecular modeling To: modeller-care(a)salilab.org Dear Sir, I have requested for Modeller 9.13 software, got License and installed ti successfully. I am following the script files and commands as per the manual exactly. But, unable to run some script files in the process of modelling. I have troubleshooted a lot and finally mailing you for your assistance. I want to do modeling using Modeller software. It gives the best possible models. I request you to kindly help me in sending modeling procedure little more in detail. I need ".py" file creation steps too. I will be highly thankful, if am done with modelling using modeller.. Awaiting your reply Thanking you, Yours faithfully, Swetha kumari K.

1 0

using Modeller for building models using contacts and secondary structures
by Adhikari, Badri (MU-Student) 06 Jan '15

06 Jan '15

Hello, I used Modeller to reconstruct around a 100 proteins with true residue-residue contacts and secondary structure information. I could reconstruct only a few proteins with high accuracy. Below is a sample script I used for Modelling. I did not use any templates. (I found that Modeller satisfies more contact restraints when I provided a template with just one residue's coordinates instead of an extended structure as a template.) I wonder why Modeller could not satisfy true contact restraints. Is there any specific way to reconstruct proteins using true residue contacts? My PY files and PIR files look like this: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Helices and Strands rsr.add(secondary_structure.strand(self.residue_range('3:', '11:'))) rsr.add(secondary_structure.strand(self.residue_range('16:', '26:'))) rsr.add(secondary_structure.alpha(self.residue_range('126:', '140:'))) # Contacts: rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CA:9'], at['CA:18']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:3'], at['CB:24']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:5'], at['CB:22']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:122'], at['CB:132']),mean=8.0, stdev=0.1)) a = MyModel(env, alnfile = '1f21.pir', # alignment filename knowns = 'empty', # codes of the templates sequence = '1f21') # code of the target a.starting_model= 1 a.ending_model = 20 a.make() C; >P1;empty structureX:empty: 1: : 152: : : :1.0: K-------------------------------------------------------------------------------------------------------------------------------------------------------* C; >P1;1f21 : : : : : : : : : KQVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGYQVE* Badri Adhikari University of Missouri ?

2 2

Error
by Sakshi Rajput 27 Dec '14

27 Dec '14

Hi, I am using Modeller9.14 and python2.7 version. When I execute the script, it shows error 'import site' failed; use -v for traceback Cannot open logfile align2d.log: Permission denied I hope you will solve my problem as soon as possible. Thanking you Yours Sincerely, Sakshi Singh -- Yours Sincerely, Sakshi Singh Research Scholar, Dept. of Molecular and Human Genetics,BHU, Varanasi, India

2 1

Re: [modeller_usage] Disulfide bridge between residues into different monomers
by bharat lal 12 Dec '14

12 Dec '14

Hi, I am working on a decameric protein and want to create disulfide bridge between cysteines of adjacent monomers. I used the following script (model-disulfide.py): # Homology modeling by the automodel classfrom modeller import * # Load standard Modeller classesfrom modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides# (this routine is empty by default):class MyModel(automodel): def special_patches(self, aln): # A disulfide between residues 8 and 45: self.patch(residue_type='DISU', residues=(self.residues['14:A'], self.residues['44:D'])) log.verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in # directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] a = MyModel(env, alnfile = 'twochain.ali', # alignment filename knowns = 'em', # codes of the templates sequence = 'query') # code of the targeta.starting_model= 1 # index of the first modela.ending_model = 1 # index of the last model # (determines how many models to calculate)a.make() # do the actual homology modeling First I tried making only one hydrogen bond between residue 14 of chain A and 44 of chain D but I am getting the following errors:- H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 model-disulfide. py'import site' failed; use -v for tracebackTraceback (most recent call last): File "model-disulfide.py", line 26, in ? a.make() # do the actual homology modeling File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 97, in make self.homcsr(exit_stage) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 436, in homcsr self.make_initial_model(aln) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 450, in make_initial_model self.generate_method(self, aln) File "H:\Modeller9.13\modlib\modeller\automodel\generate.py", line 39, in transfer_xyz mdl.create_topology(aln) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 677, in create_topology self.special_patches(aln) File "model-disulfide.py", line 10, in special_patches self.patch(residue_type='DISU', residues=(self.residues['14:A'], File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 254, in __getitem__ (self.offset, self.length, self.suffix)) File "H:\Modeller9.13\modlib\modeller\util\modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 318, in _indxres raise KeyError("No such residue: %s" % indx)KeyError: 'No such residue: 44:D' I even tried giving the residue information as: 14:A and 44:D, but still I am getting the same error (as above). Just to inform you further my template does not have cysteines for the formation of disulfide bridges, so I also generated a mutant with cysteines and tried the patch.py script: from modeller import *from modeller.scripts import complete_pdb env = environ()env.io.atom_files_directory = ['../atom_files']env.libs.topology.read(file='$(LIB)/top_heav.lib')env.libs.parameters.read(file='$(LIB)/par.lib') # Create the disulfide bond:def patches(mdl): mdl.patch(residue_type='DISU', residues=(mdl.residues['14:A'], mdl.residues['44:D']))# Read the sequence:code = 'em-2.pdb'mdl = complete_pdb(env, code, special_patches=patches) # Create the stereochemical restraintssel = selection(mdl)mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) # Calculate the energy to test the disulfide:sel.energy() This is the error I got: H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 patch.py'import site' failed; use -v for tracebackTraceback (most recent call last): File "patch.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "H:\Modeller9.13\modlib\modeller\scripts\complete_pdb.py", line 39, in complete_pdb special_patches(mdl) File "patch.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['14:A'], File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 254, in __getitem__ (self.offset, self.length, self.suffix)) File "H:\Modeller9.13\modlib\modeller\util\modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 318, in _indxres raise KeyError("No such residue: %s" % indx)KeyError: 'No such residue: 44:D' Can anybody help me in this regard? Monu

2 1