- modeller_usage - salilab.org

generating homology models of reduced disulfide bonds
by Stephanie Schaefer 02 Feb '12

02 Feb '12

Hello, I recently obtained the xray structure of my wildtype protein which I am using as my template. This protein has a redox active disulfide (an other structural disulfides). I would like to generate homology models in which the redox active disulfide bond is broken (the model would represent the cysteines in a reduced environment). I am new to modeler, but what I have done is edited the template PDB (wildtype) to remove the active site disulfide (SSbond) and then generated a homology model using the modified wt PDB as the template. Is this the correct approach to generating a reduced active site model? If this is not an acceptable approach what would you suggest? Thank you for your time, Stephanie Schaefer University of Delaware Biochemistry PhD Student 302-831-2658

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problems with filling missing residue without moving exing ones
by Francesco Pietra 02 Feb '12

02 Feb '12

I could nicely fill missing residues 519-522 and 683-684 by using the normal protocol at /wiki/Missing residue. However, as I would like the existing residues not being modified, I used a script: 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 select_atoms(self): return selection(self.residue_range('518', '521'), self.residue_range('681', '683')) a = MyModel(env, alnfile = 'alignment.ali', knowns = myPDB, sequence = 'myPDB_fill') a.starting_model= 1 a.ending_model = 1 a.make() based on the last part of the wiki. Consistently, the error is: ................................. File "fill_resid_no-move.py", line 20, in ? a.make() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 106, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 490, in _check_select_atoms atmsel = self.select_atoms() File "fill_resid_no-move.py", line 12, in select_atoms return selection(self.residue_range('518', '521'), File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 518' I tried different selections as '518', '521' always getting error in finding the first residue in this '...' list. alignment.ali is constructed, as in the wiki, of first the structure, then the sequence. At any event, the alignment.ali is the same that works well with the script that allows all atoms to move. I serched the web; hope this is no duplication. Thanks for advice francesco pietra

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libraries issue
by Francesco Pietra 31 Jan '12

31 Jan '12

Hello: with debian amd64, python 2.6, I am at filling missing residues with script 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 = 'alignment.ali', knowns = 'FlaK', sequence = 'FlaK_fill') a.starting_model= 1 a.ending_model = 1 a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.fast a.make() and command # mod9.10 fill_res.py I had some(overcome) problems of alignment. Now, suddenly: francesco@gig64:~/tmp$ mod9.10 fill_resid.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback francesco@gig64:~/tmp$ which is curious as I am at Modeller modules, so that Python's version should be immaterial. At any event, I can't install a previous version of Python. Thanks for advice francesco pietra

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(no subject)
by Francesco Pietra 31 Jan '12

31 Jan '12

Back to Modeller from a long absence, I am faced by a trivial, common issue; "no module named modeller" when running "fill_resid.py", which reads: from modeller import * from modeller.automodel import * # Load the automodel class long.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = 'alignment.ali', knowns = 'my, sequence = 'my_fill') a.starting_model= 1 a.ending_model = 1 a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.fast a.make() fill_resid.py, my.pdb, and alignement.ali are in the same dworking directory (My aim is to fill lacking residues in ltwo loops of a protein) The software is correctly installed in debian amd64: francesco@gig64:~$ which mod9.10 /usr/bin/mod9.10 francesco@gig64:~$ Thanks for advice francesco pietra

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Phosphoserine residue
by Mike Bramson 30 Jan '12

30 Jan '12

I am just getting started with Modeller, but I need to incorporate a phosphoserine residue, which Modeller cannot seem to handle by default. I have read the FAQ entry on defining new residue types, but it seems quite daunting and I do not have easy access to the needed software. I see that ten years ago, someone ran into the same problem, but as far as I can tell it was never resolved: http://salilab.org/archives/modeller_usage/2002/msg00177.html So I will ask the same question as that poor soul a decade ago: does anyone have the appropriate files for phosphoserine, and would be willing to share? Thanks, Mike Bramson

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Need Help getting started
by Henry, Marcia B 30 Jan '12

30 Jan '12

I'm a novice (biochemistry). Very little computer programming, however I can usually teach myself from tutorials. I must be missing something. I can't get through the basic example. I have my sequence in PIR format. Next, going through the example, I opened up the modeller program to get the command screen. I started by typing mod9.10 since I don't have Python installed. c:\Program Files (x86)\Modeller9.10>mod9.10 usage: mod9.10script [...] Next, I attempt to use the command "profile.build()...... and it gives me the error 'profile.build' is not recognized as an internal or external command, operable program or batch file. I have tried to put a name in the parenthesis and I get the same error. Never recognizes the "name" in the parenthesis. I have tried to look at the commands by going to the command directory, but I get the same error regardless of which command I try. Please help! I think I can proceed if I could only start.

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how to analyse the output file of align2d.py
by Naresh 30 Jan '12

30 Jan '12

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. I checked for the template sequence in the pdb_95.pir. but unfortunately I could not find any template sequence for the templates which I selected from the blast result.

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modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 3O96
by Naresh 29 Jan '12

29 Jan '12

I am getting this error when I run model-single.py I am using windows 7 OS, modeller9.10, python3 The other commands (build_profile, align2d, compare) run successfully .. C:\Program Files\Modeller9.10\bin\akt3>mod9.10 model-single.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-single.py", line 9, in ? a.make() File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 96, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 408, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 398, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller9.10\modlib\modeller\alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was n ot found in the alignment file; ALIGN_CODES( 1) = 3O96

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Import Error: No module named _modeler
by Naresh 28 Jan '12

28 Jan '12

Hi, I am new to modeller, I followed the tutorial and ran this command model-default.py I got the following error, Import Error: No module named _modeller Could you please suggest me with some best solution

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Re: [modeller_usage] Is there a way to it?
by Modeller Caretaker 11 Jan '12

11 Jan '12

On 1/10/12 7:34 PM, Ashish Runthala wrote: > Respected Sir, > Are you saying about this line? > 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)): That looks like a loop from one of the SALIGN example scripts, which simply calls SALIGN three times. If you look further down in the script you will see this: aln.salign(..., feature_weights=weights) i.e. SALIGN is being called with the weights given by the first argument in that 'for' statement above. > What do each of the 6 float constants represent? They're weights - just numbers that multiply each feature's distance matrix. The distance matrix used by SALIGN is simply a linear combination of these. > Also tell me What you exactly mean by feature_weights=[0]*6. I mean exactly what it says - that's elementary Python syntax. [0]*6 is the same as saying [0,0,0,0,0,0]. In other words, all of the features will have zero weight, so SALIGN won't calculate any of them. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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