- modeller_usage - salilab.org

Building in missing residues from a known structure
by Joshua Adelman 12 Sep '12

12 Sep '12

I've looked through the mailing list archives and online documentation, but I'm having some trouble wrapping my head around the proper way to accomplish the following. I have two PDB files of a protein in different conformations, where in one of the two PDBs, a short stretch of residues are missing, but in the other the complete coordinates in that region are known. Both PDBs have different missing residues throughout their chain, but I'm only interested at this time in modeling that small section that's present in one and not in the other. My alignment file looks something like: >P1;A structureX:A: 1 :A:149 :A:::-1.00:-1.00 ---------FIRIMVFAIYVALPIGV--------------------AGKSLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL* >P1;B structureX:B:1 :A:149 :A:::-1.00:-1.00 --------SFIRIMVFAIYVALPIGVGLWV-------------------SLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRS----LTILAVFWISLYIFVNLTSVLYL* In B the sequence `NKKL` is missing. Because they are in different conformations, I want to use the PDB for B as an initial model. In each of the PDB files, the residues follow the number in the above sequence alignment, and only contain coordinates for the residues that are not marked with a `-`. My script looks like: ----------------------------------------------------- ----------------------------------------------------- # Modeling using a provided initial structure file (inifile) 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 = ['.', '../structures'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('123', '126')) a = MyModel(env, alnfile='../sequences/alignments.ali', # alignment filename knowns='A', # codes of the templates sequence='B', # code of the target inifile='B.pdb') # use 'my' initial structure a.starting_model = 1 # index of the first model a.ending_model = 1 # index of the last model a.make() # do homology modeling ----------------------------------------------------- ----------------------------------------------------- If in my alignment file, I specify that each structure starts at residue 1, I get an error: > No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: ../structures/A.pdb However if I change the starting residue to 10 in A and 9 in B, Modeller runs, but it builds a different set of residues than I intended, because I think it is numbering the residues in sequential order as they are read in from the PDBs, ignoring the missing residues (determined by running the small script in FAQ #17). I've seen advice on renumbering residues on the mailing list, but I'm not sure if I'm missing something more basic. Any suggestions or pointers would be most appreciate. Josh

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Regarding Modelling
by Ashish Runthala 12 Sep '12

12 Sep '12

Is there a way that i can ask MODELLER to exactly copy the topology of backbone,CA atoms of all the aligned residues and model the same for the other unaligned loop chunks. But it should not add the side chains. Is there a way that the side chain addition can be stopped after the desired initial backbone, CA construction. Best Regards Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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A small query regarding modelling
by Ashish Runthala 08 Sep '12

08 Sep '12

Respected Sir, First of all, congratulations for the MODELLER's 9.11 release. I have a small query. For a considered well reliable template, is it possible that i can also use the side chain information exactly the same way from the template, i.e. MODELLER uses the complete backbone and side-chain information for the aligned residues from the considered template, and accordingly the MODELLER then predicts the left over residues through the earlier considered reliable scaffolds? Please guide me the same way. Sincerely, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Modeller 9.11 release
by Modeller Caretaker 06 Sep '12

06 Sep '12

The new version of Modeller, 9.11, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.11 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.11 is primarily a bugfix release relative to the last public release (9.10). Major user-visible changes include: # Alpha (Tru64), Itanium (ia64) and Sun Solaris binaries are no longer provided. If you wish to use Modeller on one of these machines, please use the older 9.10 version. # sequence_db objects now only store part of the sequence database in memory when using a binary (HDF5) file (databases in PIR or FASTA format still must be read in in their entirety). Functions that use sequence databases now take a window_size argument, that controls how much of the database is read into memory at one time. This results in much lower memory usage when using large databases such as UniProt. # SSBOND and CONECT records are now written to PDB files when models containing disulfides are saved. # The default behavior of automatically converting common modified residues (MSE, MEX, ABU) to their standard equivalents can now be disabled by setting env.io.convert_modres=False. See the Modeller manual for a full change log: http://salilab.org/modeller/9.11/manual/node39.html If you encounter bugs in Modeller 9.11, please see http://salilab.org/modeller/9.11/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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minimize after filling the gaps
by Mary Varughese 06 Sep '12

06 Sep '12

Hi, On building the missing residues in a protein(under the option no change to rest of the protein), could i retain the cofactors. Should i minimize the protein as a whole or build region specifically before performing any docking and simulation. I understand the building process itself perform some minimization. Isn't that enough? Thanking You, -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India

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Re: [modeller_usage] Trouble with angle restrain in chimera
by virginia miguel 04 Sep '12

04 Sep '12

João! Thank you very much for your help! that work out! Sorry to bother you again but now the error that appears is the following: File "model-multiple.py", line 17, in special_restraints feature=features.angle(a['CA:796'], TypeError: unsubscriptable object For what i can understand it does not recognize a sequence of atoms in class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) I have tried feature=features.angle(a['CA:796', 'CA:822','CA:855']), and feature=features.angle(a 'CA:796', 'CA:822','CA:855' ), but they did not worked. Do you know how could I fix this? I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) --- El lun 3-sep-12, João Rodrigues <anaryin(a)gmail.com> escribió: De: João Rodrigues <anaryin(a)gmail.com> Asunto: Re: [modeller_usage] Trouble with angle restrain in chimera Para: "virginia miguel" <virgimiguel(a)yahoo.com.ar> Cc: modeller_usage(a)salilab.org Fecha: lunes, 3 de septiembre de 2012, 17:24 Hey Virginia, You have one less indentation level in that line. Python then considers it out of the class MyModel and thus, rsr is not previously declared. Just hit tab/4 spaces behind rsr.add and it should work. Best, João No dia 3 de Set de 2012 22:45, "virginia miguel" <virgimiguel(a)yahoo.com.ar> escreveu: Hi everyone, I am trying to build a chimera protein based on two known structures that do not overlap, and I am trying to specify an angle restrain between the two domains that are model to give information of their relative orientation obtained experimentally using this script: # Homology modeling with multiple templates 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' class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) rsr.add(f) a = MyModel(env, alnfile = 'align2.ali', # alignment filename knowns = ('2OK2','1FW6','1E3M'), # codes of the templates sequence = 'PAOI') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() but I get this error: File "model-multiple.py", line 12, in ? class MyModel(automodel): File "model-multiple.py", line 21, in MyModel rsr.add(f) NameError: name 'rsr' is not defined So I do not know what I am missing....if someone can help me! Thank you in advance! Virginia. I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage -----Adjunto en línea a continuación----- _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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Trouble with angle restrain in chimera
by virginia miguel 03 Sep '12

03 Sep '12

Hi everyone, I am trying to build a chimera protein based on two known structures that do not overlap, and I am trying to specify an angle restrain between the two domains that are model to give information of their relative orientation obtained experimentally using this script: # Homology modeling with multiple templates 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' class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) rsr.add(f) a = MyModel(env, alnfile = 'align2.ali', # alignment filename knowns = ('2OK2','1FW6','1E3M'), # codes of the templates sequence = 'PAOI') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() but I get this error: File "model-multiple.py", line 12, in ? class MyModel(automodel): File "model-multiple.py", line 21, in MyModel rsr.add(f) NameError: name 'rsr' is not defined So I do not know what I am missing....if someone can help me! Thank you in advance! Virginia. I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)

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GNUPLOT using the command please sent to email , how to use gnuplot
by Nandha Kumar 30 Aug '12

30 Aug '12

-- nandhakumar

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modeller9.10 using error on display
by Nandha Kumar 24 Aug '12

24 Aug '12

cannot open logfile script1.log;permission denied ( please sent solutions) i am using windows 8 os ,python 3.2.3 installed ) -- nandhakumar

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Modelling a heterodimeric structure using heterodimeric template
by Rakshambikai R 17 Aug '12

17 Aug '12

Dear Sir/Madam, I am modelling a heterodimeric structure from a heterodimeric template. I tried modelling it using separate chains but I am facing difficulty in building the complex. Is it possible to build a model using the complex structure as a whole (I did see a mention of using "/" as a chain separater in your archives for a homodimer)? If so, how do I specify the regions to be modelled?I have put an example of the regions: query chain 1 length: 878 region aligning:1-827 template: chain B; actual region in pdb: 362-1335 ; region aligning;427-1335 query chain 2: length: 901 length aligning:59-848 template: chain A; actual region in pdb:1-855; length aligning;150-854 Awaiting your response. Thanking you, RAKSHAMBIKAI R PhD student Prof N Srinivasan's lab MBU,IISc Ph:080-22932837 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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