February 2012 - modeller_usage

error in Virutualbox
by albert 18 Feb '12

18 Feb '12

Hello: I am trying to run modeller with following scrips, but it said in terminal: ----log------------ EV/1% Traceback (most recent call last): File "model.py", line 6, in <module> j = job() File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 24, in __init__ self.host = socket.gethostbyname_ex(socket.gethostname())[-1][0] socket.gaierror: [Errno -2] Name or service not known ----------scrips-------------------------------- from modeller import * from modeller.automodel import * from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) env = environ(rand_seed=-6666, restyp_lib_file='$(LIB)/restyp.lib', copy=None) log.verbose() # Give less weight to all soft-sphere restraints: env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['/usr/lib/modeller9.10/bin', '/media/sf_Documents/EPFL/02-modeller/EV/1'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile='test.ali', knowns=('MyA'), sequence='test', a.starting_model = 1 a.ending_model = 200 a.use_parallel_job(j) a.make()

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Re: [modeller_usage] to generate the DOPE plot
by Modeller Caretaker 17 Feb '12

17 Feb '12

On 2/17/12 3:28 PM, Xiao-Ping Zhang wrote: > Thank you for your reply. I used RPM. So the problem is "Standard" or > "No-standard" python. > > What do you mean Standard or Non-standard? As I said in my previous email, by "standard" I mean the Python included with Fedora. This is /usr/bin/python. You said you had several other versions of Python installed in /usr/local/. Fedora packages don't install there, hence "non-standard". These packages won't work with Modeller unless you set PYTHONPATH accordingly. rpm -ql modeller | grep site-packages will show you the directories where Modeller is installed for each standard version of Python. Note also that if your Python is 32-bit, you need the 32-bit version of Modeller (ditto for 64-bit). 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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to generate the DOPE plot
by Xiao-Ping Zhang 17 Feb '12

17 Feb '12

Hi, modellers, I installed both "python-matplotlib" and "gnuplot" on my Fedora 13. My system have three versions of python: python2.6: /usr/lib/python2.6/ python2.3: /usr/local/lib/python2.3 python2.7 /usr/local/lib/python2.7 matplotlib is under python2.6 /usr/lib/python2.6/site-packages/matplotlib #################### the command "mod9.9 plot_profile.py" gives the following error: Traceback (most recent call last): File "plot_profiles.py", line 1, in ? import pylab ImportError: No module named pylab ##################### the command 'gnuplot "TvLDH.profile" using 1:42 with lines' gives this error: 1 MET 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -0.29E-01 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -0.29E-01 ^ "TvLDH.profile", line 8: invalid command ################## these are python executables: [root@localhost bin]# ls -l /usr/local/bin/python* -rwxr-xr-x. 2 root root 4621643 Jul 7 2011 /usr/local/bin/python -rwxr-xr-x. 1 root root 3122405 Oct 27 2010 /usr/local/bin/python2.3 -rwxr-xr-x. 2 root root 4621643 Jul 7 2011 /usr/local/bin/python2.7 -rwxr-xr-x. 1 root root 1624 Jul 7 2011 /usr/local/bin/python2.7-config lrwxrwxrwx. 1 root root 16 Jul 7 2011 /usr/local/bin/python-config -> python2.7-config [root@localhost bin]# ls -l /usr/bin/python* -rwxr-xr-x. 2 root root 6088 Jun 4 2010 /usr/bin/python lrwxrwxrwx. 1 root root 6 Sep 28 2010 /usr/bin/python2 -> python -rwxr-xr-x. 2 root root 6088 Jun 4 2010 /usr/bin/python2.6 -rwxr-xr-x. 1 root root 1418 Jun 4 2010 /usr/bin/python2.6-config lrwxrwxrwx. 1 root root 16 Sep 28 2010 /usr/bin/python-config -> python2.6-config How to fix my system to make the gnuplot and matplotlib work? Thank you. XP

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error
by Rana Adnantahir 16 Feb '12

16 Feb '12

Dear Sir I am the student of bioinformatics and i am working on MODELLER for comparative modeling. I prepared all the inputs of Modeller but when i run the query "mod9.10 model-default.py" then it gives an error message [' import site' failed; use -v for traceback cannot open logfile model-default.py: permission denied] Please kindly help me. Adnan Tahir

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MAPRES limit
by Johs, Alexander 14 Feb '12

14 Feb '12

Hi, I'm trying to model a protein with a cyanocobalamin cofactor. I have included CHARMM topology and parameter files using the corresponding .append commands, created a custom residue for the cyanocobalamin in restyp.lib and added atomic radii. Looks like there is a limit on the number of atoms per residue... How can I increase this limit? Here's the log output: ---- Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4242516 4143.082 4.046 openf___224_> Open ${LIB}/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open top_cyanocob.rtf read_to_238_> Reading CHARMM residue topology file version: 27 1 read_to_223E> Internal error: array too small: MAPRES current maximum, current need: 100 101 ---- Thanks, Alex

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run two file or two restrained together
by Pablo Fernandez Millan 13 Feb '12

13 Feb '12

Hello, I try to modeller my protein, and I had two different files which succerful good independely, but I need to uses the restrained from the firts file in combination of the symetry restrained of the second file. Down, I just copied the type file I have used. How can I run both at the same time? thank you !! # Addition of restraints to the default ones 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 # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr') # Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('20:', '30:'))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('1:', '6:'))) rsr.add(secondary_structure.strand(self.residue_range('9:', '14:'))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'], sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: # rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'], # sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CA:35'], at['CA:40']), mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # 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 ---------------------------------------------------------- # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '2abx', # codes of the templates sequence = '1hc9') # 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 *Example: examples/automodel/twochain.ali<http://salilab.org/modeller/examples/automodel/twochain.ali> * C; example for building multi-chain protein models >P1;2abx structureX:2abx: 1 :A:74 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;1hc9 sequence:1hc9: 1 :A:148:B:undefined:undefined:-1.00:-1.00 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG/ IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG*

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Re: [modeller_usage] modeling of movement of domain
by Ahmadreza Mehdipour 11 Feb '12

11 Feb '12

Hi Ben My script is as follows: from modeller import * env = environ() env.io.atom_files_directory = ['.'] mdl = model(env, file='test1') # Keep two domains rigid: r1 = rigid_body(mdl.residue_range('48:A', '124:A')) r2 = rigid_body(mdl.residue_range('132:A', '205:A')) r3 = rigid_body(mdl.residue_range('212:A', '304:A')) mdl.restraints.rigid_bodies.append(r1) mdl.restraints.rigid_bodies.append(r2) mdl.restraints.rigid_bodies.append(r3) # put the restraints on domains at=mdl.atoms mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CG2:128:A'], at['OD1:148:A']), mean=40, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:185:A']), mean=43, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:160:A']), mean=45, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:201:A']), mean=32, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:106:A'], at['O1:185:A']), mean=25, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:106:A'], at['O1:160:A']), mean=35, stdev=0.1)) mdl.write(file='test.pdb') Thanks Reza

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(no subject)
by ARVIND PAL 10 Feb '12

10 Feb '12

I have a problem. when i am using cryo-em. plz tell me what is the format of current working directory.

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modeling of movement of domain
by Ahmadreza Mehdipour 10 Feb '12

10 Feb '12

Hello I am working with a protein having three domains and two hinge between them. I have x-ray structure of protein. now, I want to keep the domains rigid and then apply some experimental data(EPR distances) in order to have new conformation. I use rigid body command to keep domains rigid and then use restraints to define the distances. But modeller does not apply the distance. What is the problem and how I can apply such restraints. Thanks Reza

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Re: [modeller_usage] Regarding Scoring Parameters
by Mensur Dlakic 09 Feb '12

09 Feb '12

I am not sure I understand your question, and I will assume that by "normal set of these parameters" you mean "unifying set across different programs". If that's your question, the answer is that there is no common set of lambda and kappa parameters (extreme value distribution factors) between different programs, or even within the same program. The values of these parameters are dependent on the scoring scheme used, so when you change the substitution matrix in PSI-BLAST, they will change. If you calibrate HHPRED models in "local" and "global" modes, you'll get different kappa and lambda values, and the same is true if you change other program parameters that affect the scoring and alignments. If you take a sequence (or profile) with certain composition and length and calculate lambda and kappa, they will be different from the next sequence depending on its length and sequence composition. In an extreme case, you can even take the same HHPRED profile and calibrate it against two different databases, for example the one provided with the program, and another database with similar number of profiles, and you'll most likely get different extreme value distribution parameters. Before anyone freaks out because of this uncertainty, it bears mentioning that most of these changes would affect only borderline matches. This is to say that you can't determine these parameters in one program and then use them with others. You can't even determine these parameters for local scoring and then use them for global scoring with the same program. In short, extreme value distribution parameters are both sequence-, program- and scoring parameter-specific. Hope this helps, Mensur At 12:16 AM 2/9/2012, you wrote: >Dear Modellers, >For E-value and alignment scoring systems, we use the parameters >lambda and K. >Specifying these scores is must for a scoring system. So what is/are >the normal set of these parameters used in PSI-BLAST/CS-BLAST/HHPRED >or other profile inclusion based template searching methods? >Tell me the commonly used values for these two parameters lambda and >K for the calculation of alignment scores. > >Thanks >Ashish > >Ashish Runthala, >Lecturer, Structural Biology Cell, >Biological Sciences Group, >BITS, Pilani >Rajasthan, INDIA >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >https://salilab.org/mailman/listinfo/modeller_usage ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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