- modeller_usage - salilab.org

stuck even before begining - how to create the .ali file
by Ariel Bensimon 18 Apr '07

18 Apr '07

I would like to use MODELLER to structurally align a protein domain with a known PDB. But I am stuck. I could even create the basic .ali file. Trying using the manual. Couldn't find the basic start of things Thanx , A.

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using model-addrsr in modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-addrsr. By predicting secondary structure, between residues "305-318" is alpha-helix. I modified the model-addrsr.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion. Thanks. 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' class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) a = mymodel(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling The error: File "modelrsr.py", line 14 rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) ^ IndentationError: unindent does not match any outer indentation level The .log file: MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 22:15:53

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using model-loop-refine in Modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-loop-refine. I modified the model-loop-refine.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion. Thanks. from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('53:', '67:') (self.residue_range('89:', '96:') (self.residue_range('118:', '144:') (self.residue_range('166:', '177:') (self.residue_range('199:', '221:') (self.residue_range('243:', '254:')) a = myloop(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do modeling and loop refinement This is the error: File "model-loop-refine.py", line 21 m = myloop(env, ^ SyntaxError: invalid syntax

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by Pankaj R. Daga 17 Apr '07

17 Apr '07

Hey jin lian I guess you need to remove the parentheses before "self.residue_range". They are not necessary or else, you need to compete those parentheses. This is not the problem of modeller, rather its mainly related to python script. hope this helps. Cheers PanDa =================================================================== If your ship doesn't come in, swim out to it.......Jonathan Winters =================================================================== Pankaj R. Daga | Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | ===================================================================

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by Pankaj R. Daga 17 Apr '07

17 Apr '07

Hey jin lian I guess you need to remove the parentheses before "self.residue_range". They are not necessary or else, you need to compete those parentheses. This is not the problem of modeller, rather its mainly related to python script. hope this helps. Cheers PanDa =================================================================== If your ship doesn't come in, swim out to it.......Jonathan Winters =================================================================== Pankaj R. Daga | Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | =================================================================== ----- Original Message ----- From: <modeller_usage-request(a)salilab.org> To: <modeller_usage(a)salilab.org> Sent: Tuesday, April 17, 2007 5:32 AM Subject: modeller_usage Digest, Vol 6, Issue 33 > 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: Psi and Phi Dihedral Restraints (Modeller Caretaker) > 2. using model-loop-refine in Modeller9v1 (jinlian05(a)lzu.cn) > 3. Re: using model-loop-refine in Modeller9v1 (Charlie Allerston) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Apr 2007 23:40:48 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] Psi and Phi Dihedral Restraints > To: Brandon Mills <bmm25(a)pitt.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <46246BF0.1030209(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Brandon Mills wrote: >> I have recently been toying with certain restraints in my .rsr files, >> and I have a couple questions. Can someone elaborate on the effect of >> restraints which contain eight atoms and a multiple of six parameters >> (I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4 >> atoms and 28 parameters? What exactly are these parameters? Also, is >> there an easy way to pick out the psi and phi restraints out of the >> general dihedral restraints? Thanks in advance! > > See http://salilab.org/modeller/9v1/manual/node382.html for a > description of the restraints file format. The second column (restraint > form) is the one you're probably interested in (it will be 9 for > multi-binormal (phi/psi) restraints). There is a multiple of six > parameters for each of these because there are six parameters for each > well in the function (weight, 2 means, 2 stdevs, and a correlation; see > http://salilab.org/modeller/9v1/manual/node91.html) > > The other restraints you mention are almost certainly cubic spline > restraints (form 10). These are used because it is more efficient to > evaluate a cubic spline than a multiple Gaussian. > > 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: Tue, 17 Apr 2007 16:49:01 +0800 > From: "" <jinlian05(a)lzu.cn> > Subject: [modeller_usage] using model-loop-refine in Modeller9v1 > To: modeller_usage(a)salilab.org > Message-ID: <376799741.12858(a)st.lzu.edu.cn> > Content-Type: text/plain > > Hi, > I am new to modeller and I have trouble creating a homology model of a > protein using model-loop-refine. I modified the model-loop-refine.py script as > shown below and I got error messages. I would appreciate it if any one > can give me any suggestion. > Thanks. > > from modeller import * > from modeller.automodel import * > > log.verbose() > env = environ() > > env.io.atom_files_directory = './:../atom_files' > > # Create a new class based on 'loopmodel' so that we can redefine > # select_loop_atoms > class myloop(loopmodel): > # This routine picks the residues to be refined by loop modeling > def select_loop_atoms(self): > return selection(self.residue_range('53:', '67:') > (self.residue_range('89:', '96:') > (self.residue_range('118:', '144:') > (self.residue_range('166:', '177:') > (self.residue_range('199:', '221:') > (self.residue_range('243:', '254:')) > > a = myloop(env, > alnfile = 'seg.ali', # alignment filename > knowns = '1u19A', # codes of the templates > sequence = 'mrg1', # code of the target > loop_assess_methods=assess.DOPE) # assess each loop with DOPE > a.starting_model= 1 # index of the first model > a.ending_model = 1 # index of the last model > > a.loop.starting_model = 1 # First loop model > a.loop.ending_model = 2 # Last loop model > > a.make() # do modeling and loop refinement > > This is the error: > File "model-loop-refine.py", line 21 > m = myloop(env, > ^ > SyntaxError: invalid syntax > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 17 Apr 2007 10:32:29 +0000 > From: "Charlie Allerston" <charlieboyblue(a)hotmail.com> > Subject: Re: [modeller_usage] using model-loop-refine in Modeller9v1 > To: jinlian05(a)lzu.cn, modeller_usage(a)salilab.org > Message-ID: <BAY117-F1818D25C2653CF5F52AE3CDD510(a)phx.gbl> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: http://salilab.org/archives/modeller_usage/attachments/20070417/32969431/at… > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 6, Issue 33 > ********************************************* > >

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-loop-refine. I modified the model-loop-refine.py script as shown below and I got error messages. About an hour before, I got your repaly of the 'using model-loop-refine in Modeller9v1', you sent me a URL 'http://salilab.org/archives/modeller_usage/attachments/20070417/32969431/at…'. But I can not understand it. Could you explain it again for me? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('53:', '67:') (self.residue_range('89:', '96:') (self.residue_range('118:', '144:') (self.residue_range('166:', '177:') (self.residue_range('199:', '221:') (self.residue_range('243:', '254:')) a = myloop(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do modeling and loop refinement This is the error: File "model-loop-refine.py", line 21 a = myloop(env, ^ SyntaxError: invalid syntax This is the .log contents: MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 19:12:02

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Psi and Phi Dihedral Restraints
by Brandon Mills 16 Apr '07

16 Apr '07

Hello All, I have recently been toying with certain restraints in my .rsr files, and I have a couple questions. Can someone elaborate on the effect of restraints which contain eight atoms and a multiple of six parameters (I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4 atoms and 28 parameters? What exactly are these parameters? Also, is there an easy way to pick out the psi and phi restraints out of the general dihedral restraints? Thanks in advance! Sincerely, Brandon Mills -- Brandon Mills bmm25(a)pitt.edu (814) 360-1382 Lab: 338, Eberly Hall

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Add rigid bodies and CA-CA restraints
by Gregoire Depret 10 Apr '07

10 Apr '07

Hello, I have built a model and I want it to satisfy some CA-CA restraints. In order to do so, I've added some restraints with the command "rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['CA:893:C'],at['CA:184:B']),mean=10.0, stdev=0.1))" and some restraints on secondary structure to avoid unwinding of alpha helix. Actually these restraints caused kinks in alpha-helices that are known to span the membrane. To avoid that kind of kinks I want to treat the helices as rigid bodies. First I tried to add rigid bodies in the same script a = mymodel(env, alnfile = 'align.pir', # alignment filename knowns = '2OXS', # codes of the templates sequence = 'mytemplate ') # code of the target r = rigid_body(a.residue_range('180:B', '200:B')) s = rigid_body(a.residue_range('890:C', '900:C')) a.restraints.rigid_bodies.append(r) a.restraints.rigid_bodies.append(s) But in this case, MODELLER doesn't recognize the residue range, and raises the error "No such Residues 180:B". I have checked in previous models; the residues are there. I also tried to start from an existing model and applied molecular dynamics on it, like it is described in optimize.py. I have succeeded in defining the rigid body on my initial model but the applied restraints aren't strong enough to move my intitial model. In addition the MD partially unwinds the secondary structure of my model. Here is the script I used that differs from the manual. # Keep residues 1-10 rigid: r = rigid_body(mdl.residue_range('277:B', '318:B')) s = rigid_body(mdl.residue_range('972:C', '1014:C')) mdl.restraints.rigid_bodies.append(r) mdl.restraints.rigid_bodies.append(s) # Select all atoms: atmsel = selection(mdl) # Generate the restraints: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr') a = mdl.atoms mdl.restraints.add(forms.upper_bound(group=physical.xy_distance, feature=features.distance(a['CA:343:B'], a['CA:986:C']), mean=18., stdev=0.1)) Thus I have two questions : Is it possible, in the same script, to add rigid body restraints and then do the modelling or applying rigid bodies is only possible on an already existing model? To satisfy my restraints which approach is the best : add my CA-CA restraint, my rigid body definition and make the homology modelling at the same time or do a MD on an existing model? Suggestions are welcome. Many Thanks, Depret Grégoire

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Rigid ligand
by dimitry.a.suplatov 10 Apr '07

10 Apr '07

I have a big lignad (Oxidised penicillin G) I want to model with. Is there a special command to make it rigid during the modeling process? Thanks

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User defined restraints
by Dimitry.A.Suplatov 09 Apr '07

09 Apr '07

Hello. I want to define restraints while modeling with ligand and I want to define different restraints. I use the following script --------------------------------------------------------------------------------------------- ... class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('OD1:282:B', 'CA:765:B'), ('OD2:282:B', 'CA:765:B'), ('OD1:285:B','CA:765:B'), ('OD2:460:B', 'CA:765:B'), ('OE2:152:A', 'CA:765:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.5, stdev=0.1)) def special_restraints(self, aln): rsr2 = self.restraints for ids1 in (('OE2:152:A', 'CA:765:B')): atoms = [self.atoms[j] for j in ids1] rsr2.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.3, stdev=0.1)) env = environ() env.io.hetatm = True env.io.water = True ... --------------------------------------------------------------------------------------------- Then I get this error -------------------------------------------------------------------------------------------- Traceback (most recent call last): File "model-ca.py", line 32, in ? a.make() File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 108, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 427, in homcsr self.mkhomcsr(selection(self), aln) File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 537, in mkhomcsr self.special_restraints(aln) File "model-ca.py", line 19, in special_restraints atoms = [self.atoms[j] for j in ids1] File "C:\Program Files\Modeller9v1\modlib\modeller\coordinates.py", line 127, in __getitem__ (self.offset, self.length, self.suffix)) File "C:\Program Files\Modeller9v1\modlib\modeller\util\modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "C:\Program Files\Modeller9v1\modlib\modeller\coordinates.py", line 40, in _indxatm newindx = _modeller.indxatm2(indx+suffix, self.modpt) - 1 - offset _modeller.error: indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: O --------------------------------------------------------------------------------------------- I am using python for the first time so that must be some problem with the script. Do you have any suggestions? Thank you!

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