- modeller_usage - salilab.org

How should I fill in the missing rsidues with the same chain id, resnumber and HETATM keeping?
by wayj86 wayj86 16 Mar '10

16 Mar '10

Dear all, I am trying to fix a protein with 6 missing aa. This protein has a resid from 500 to 650, with three HETATM residues (N-glycan) from 800 to 802 ( discontinuous with the protein resnumber). Here is my script to run modeller: *First step: to build a model with blank chain ID and resnumber from 1 to 150:* # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['./', ':../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True env.patch_default = False class MyModel(automodel): def select_atoms(self): # Select residues 41 and 46 (PDB numbering) return selection(self.residue_range('41', '46')) a = MyModel(env, alnfile = 'xy.pir', # alignment filename knowns = 'x', # sequence = 'y', assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) By running this script I did got a model with missing residues fixed and HETATM keeping, but the chain ID was blank (because only one chain was built), and the resnumber was from 1 to 154. I did hope to keep the original chain ID and the resnum, so I try the rename_segments, like: *Second step: reassign the chain ID and resnumber:* # Example for: model.rename_segments() # This will assign new PDB single-character chain id's to all the chains # in the input PDB file (here there are two 'chains': protein and the HETATM # water molecules). from modeller import * # Read the MODEL with all HETATM and water records (so there are two 'chains'): env = environ() env.io.atom_files_directory = ['./', ':../atom_files'] env.io.hetatm = True mdl = model(env, file='y') # Assign new segment names and write out the new model: mdl.rename_segments(segment_ids='A', renumber_residues=[500, 650]) mdl.write(file='y.ini') Now in the final model y.ini the chain ID was defined as "A", and resnum was from 500 to 650. However, the HETATM residues was from 651 to 653, but not 800 to 802. So should I modify my scripts to fix the protein and keeping its original chain ID, resnumber and HETATM residues? Thank you very much for your attention. P.S. The HETATM residues are also in chain A, the same chain with the protein. -- Be the change you want to see in the world.

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Refine segments of a crystal structure
by Baptiste Legrand 16 Mar '10

16 Mar '10

Hi all, Is it possible to refine protein segments from a crystal structure using modeller as we can do for models (but in this case, without providing alignment and template files) ? Thanks. Best wishes, Baptiste

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alignment with modeller
by Knut J Bjuland 16 Mar '10

16 Mar '10

I used multiple alignment with protein sequence to get a better alignment with a template. Is this a good practice. What are the recommende settings in salign to get the best possible alignment.

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HETERODIMER GENERATION
by Ajeeta kaushiki 16 Mar '10

16 Mar '10

Hi I have to generate a hetero dimer . The entire length of protein is 1500 amino acid . The first dimer is from 150-410 aa and next one is from 786-1188 aa , I have modelled this two domains separately , Now I have to map it on a known Homo Dimer present in the template pdb to generate as a heterodimer . Kindly guide or is there any other way to merge the coordinates . Thanks & Regards Ajeeta

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question on mutate monomers script
by Andrew Voronkov 11 Mar '10

11 Mar '10

Dear Modeller users, I am trying to mutate several aminoacids in the PDB file. I ve used the scrtipt (mutate.py) attached for this, but I get the error given below. What can be the problem? As I understand I need only PDB file for this script execution. Do I need to write path to the libraries in the explicit way or it should get it from the environment setup? I haven't specified the full path. Sincerely yours, Andrew :~/Mutate> mod9v7 mutate.py 'import site' failed; use -v for traceback warning: Non-ASCII character '\xe2' in file mutate.py on line 11, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details File "mutate.py", line 11 env.libs.topology.read(file=’$(LIB)/top_heav.lib’) ^ SyntaxError: invalid syntax edward@29:~/Mutate> Скачать присоединенный файл (mutate.py): # Example for: selection.mutate() # This will read a PDB file, change its sequence a little, build new # coordinates for any of the additional atoms using only the internal # geometry, and write the mutant PDB file. It can be seen as primitive, # but rapid comparative modeling for substitution mutants. For insertion # and deletion mutants, follow the standard comparative modeling procedure. from modeller import * env = environ() env.io.atom_files_directory = ['.', '../atom_files'] # Read the topology library with non-hydrogen atoms only: env.libs.topology.read(file=’$(LIB)/top_heav.lib’) # To produce a mutant with all hydrogens, uncomment this line: #env.libs.topology.read(file=’$(LIB)/top_allh.lib’) # Read the CHARMM parameter library: env.libs.parameters.read(file=’$(LIB)/par.lib’) # Read the original PDB file and copy its sequence to the alignment array: code = ’1ijy’ aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) # Select the residues to be mutated: in this case all ASP residues: sel = selection(mdl).only_residue_types(’ASP’) # The second example is commented out; it selects residues ’1’ and ’10’. #sel = selection(mdl.residues[’1’], mdl.residues[’10’]) # Mutate the selected residues into HIS residues (neutral HIS): sel.mutate(residue_type=’ASN’) # Add the mutated sequence to the alignment arrays (it is now the second # sequence in the alignment): aln.append_model(mdl, align_codes=’1ijy-1’) # Generate molecular topology for the mutant: mdl.clear_topology() mdl.generate_topology(aln[’1ijy-1’]) # Transfer all the coordinates you can from the template native structure # to the mutant (this works even if the order of atoms in the native PDB # file is not standard): mdl.transfer_xyz(aln) # Build the remaining unknown coordinates for the mutant: mdl.build(initialize_xyz=False, build_method=’INTERNAL_COORDINATES’) # Write the mutant to a file: mdl.write(file=’1ijy-1.atm’)

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Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 31
by Ashish Runthala 05 Mar '10

05 Mar '10

Ajeeta First of all you didn't tell about how you got the information about this heterodimer. I believe you have just checked the invert sequence similarity. If not, give the template(s) you have considered. For sure there is a solution. I have seen such data and got reasonably high accuracy on it. Your target sequence length is very high making it a a difficult target. But some methodologies you can apply to see it. Good Luck, Ashish ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, March 5, 2010 3:21:49 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 9, Issue 31 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: special restrains for aromatic packing interactions (Modeller Caretaker) 2. Re: Windows 7 (Joel Tyndall) 3. Re: Solving modeller problem-reg (Modeller Caretaker) 4. HETERODIMER GENERATION (Ajeeta kaushiki) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Mar 2010 07:51:37 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Thomas Evangelidis <tevang3(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] special restrains for aromatic packing interactions Message-ID: <4B8E8589.3000503(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/2/10 11:19 AM, Thomas Evangelidis wrote: > With respect to my second question, how long do you advice me to set the > distance between 2 atoms that are supposed to form an H-bond? We use 3.5A in our own code, but I recommend you try some reasonable-looking values and look at your results for artifacts. 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, 4 Mar 2010 16:06:27 +1300 From: Joel Tyndall <joel.tyndall(a)otago.ac.nz> To: Tom Venken <tom.venken(a)student.kuleuven.be>, "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Windows 7 Message-ID: <4528F8D469BACC498077D350651A728530D32519CB(a)MAIL2.registry.otago.ac.nz> Content-Type: text/plain; charset="iso-8859-1" I have installed it ...shouldn't be any issues. Just try it. Pretty sure it will work. ( ican test it if you really want) _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box?56 Dunedin 9054 New Zealand?? Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta?56 Otepoti 9054 Aotearoa Ph / Waea?????????????? +64 3 4797293 Fax / Waeawhakaahua???? +64 3 4797034 -----Original Message----- From: modeller_usage-bounces(a)salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Tom Venken Sent: Wednesday, 3 March 2010 10:51 p.m. To: modeller_usage(a)salilab.org Subject: [modeller_usage] Windows 7 Hello, At our university we are in the process of migrating our computers from Windows XP to Windows 7. I found no information about the compatibility of Modeller with Windows 7 in the release notes and I couln't find anything in the mailing list either. So does anyone know if Modeller is compatible with Windows 7, i.e. if someone has tested this OS? Kind regards, Tom _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Thu, 04 Mar 2010 08:13:32 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> To: ithaya raja <ithayaraja01(a)yahoo.co.in> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] Solving modeller problem-reg Message-ID: <4B8FDC2C.3010400(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/28/10 8:40 AM, ithaya raja wrote: > I did align my target to the template by using align2d command the > alignment file had been successfully created. executing py model script, > it is showing mod9v7.exe error sending report and the modeller > simultaneously stopped. So i need your help to understand the problem > what could be? and let me know how to solve the problem else any other > alternative...? It sounds like you are on a Windows system, and the Modeller binary crashed. This could be due either to a problem with your machine's hardware (e.g. faulty memory) or a bug in Modeller. You can check for bad hardware by trying the same script on a different machine. If that still crashes, it's likely a bug in Modeller - in that case I would need to be able to reproduce the problem in order to fix it, so would need you to send me exactly the same input files you're using when the crash occurs. 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: Fri, 5 Mar 2010 15:21:47 +0530 From: Ajeeta kaushiki <ajeetakaushiki(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] HETERODIMER GENERATION Message-ID: <e9cdb5fa1003050151p21ed05e4k661c7dbacca6f580(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi I have to generate a hetero dimer . The entire length of protein is 1500 amino acid . The first dimer is from 150-410 aa and next one is from 786-1188 aa , I have modelled this two domains separately , Now I have to map it on a known Homo Dimer present in the template pdb to generate as a heterodimer . Kindly guide or is there any other way to merge the coordinates . Thanks & Regards Ajeeta

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Windows 7
by Tom Venken 05 Mar '10

05 Mar '10

Hello, At our university we are in the process of migrating our computers from Windows XP to Windows 7. I found no information about the compatibility of Modeller with Windows 7 in the release notes and I couln't find anything in the mailing list either. So does anyone know if Modeller is compatible with Windows 7, i.e. if someone has tested this OS? Kind regards, Tom

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Re: [modeller_usage] Solving modeller problem-reg
by Modeller Caretaker 04 Mar '10

04 Mar '10

On 2/28/10 8:40 AM, ithaya raja wrote: > I did align my target to the template by using align2d command the > alignment file had been successfully created. executing py model script, > it is showing mod9v7.exe error sending report and the modeller > simultaneously stopped. So i need your help to understand the problem > what could be? and let me know how to solve the problem else any other > alternative...? It sounds like you are on a Windows system, and the Modeller binary crashed. This could be due either to a problem with your machine's hardware (e.g. faulty memory) or a bug in Modeller. You can check for bad hardware by trying the same script on a different machine. If that still crashes, it's likely a bug in Modeller - in that case I would need to be able to reproduce the problem in order to fix it, so would need you to send me exactly the same input files you're using when the crash occurs. 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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special restrains for aromatic packing interactions
by Thomas Evangelidis 03 Mar '10

03 Mar '10

Dear Modellers, I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic: http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_… I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here: http://salilab.org/modeller/manual/node196.html Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome. thanks, Tom

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ligand desgin
by Knut J Bjuland 02 Mar '10

02 Mar '10

I am using a model designed with modeller to do docking. Howevere there is problem with ligand design. The ligand is gogin to be 4 peptides long and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other postion should be any amino acid. How can I design a peptide with 20**3 different amino acids. Or can you point me to a software that do ligand desing or a good database. Knut J _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

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