- modeller_usage - salilab.org

Re: [modeller_usage] How to use MODELLER as an ordinary Python module?
by Modeller Caretaker 21 Feb '12

21 Feb '12

On 2/21/12 7:34 AM, Desmond Kho wrote: > I had tried /python plot_profiles.py/ but nothing seem to be happen. > No file was generated. > Following was the only log shown in the cmd prompt before it stop. > > MODELLER 9.9, 2011/03/29, r7963 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS OK, the fact that you're seeing the Modeller header means that everything is working correctly. I don't know why you're not seeing any output files - perhaps you're looking in the wrong place for them - but you would see an error message if something went wrong. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

1 0

How to use MODELLER as an ordinary Python module?
by Desmond Kho 21 Feb '12

21 Feb '12

Hi, I have problem with ' 'import site' failed' when I run plot_profiles.py script. File "plot_profiles.py", line 1, in ? import pylab ImportError: No module named pylab I have all Python2.6, Matplodlib, NumPy, SciPy installed. I read about "Known issues and questions with 9.10", but can't find the instructions for running Modeller with Python. May I know how to run Modeller with pyhton beside the mod9.10 script? Thanks.

2 1

energy function scaling factors
by Armin Meier 20 Feb '12

20 Feb '12

Hi Modellers, MODELLER provides a scaling option for energy function terms via e.g.: env.schedule_scale=physical.values(default=1.0, ca_distance=2) In this case, ca_distances are upscaled. If a CA-CA distance is described by a single Gaussian, its restraint is as in http://salilab.org/modeller/manual/node469.html#SECTION001332100000000000000 When scaling CA-CA distances by factor 2, is then "c" (and dc/df) simply multiplied by 2? Thanks for elucidation

2 1

Confusion between two models
by hari krishna 19 Feb '12

19 Feb '12

Dear All, I am trying to model a protein containing 859 amino acids. After loop modeling and refinement of two different models, I have doubt in chosing which model for further usage.. Becuase the stereochemical quality was good for one model (85% in favorable region) and for the second model its about 65%. Except this all other parameters like Z-score, energy, residue error plot and DOPE score favors the second model. In this case which one i need to choose. Please help me in this regard. I am attaching the procheck program results. Also the second model superimpose well to their homology proteins compared to the first model MODEL 1 +----------<<< P R O C H E C K S U M M A R Y >>>----------+ | | | input_atom_only.pdb 2.5 858 residues | | | *| Ramachandran plot: 85.4% core 11.4% allow 2.1% gener 1.1% disall | | | *| All Ramachandrans: 49 labelled residues (out of 854) | +| Chi1-chi2 plots: 5 labelled residues (out of 502) | | Main-chain params: 6 better 0 inside 0 worse | | Side-chain params: 5 better 0 inside 0 worse | | | *| Residue properties: Max.deviation: 15.7 Bad contacts: 57 | *| Bond len/angle: 10.7 Morris et al class: 1 1 3 | | | | G-factors Dihedrals: -0.07 Covalent: -0.36 Overall: -0.18 | | | | M/c bond lengths: 97.8% within limits 2.2% highlighted | *| M/c bond angles: 90.5% within limits 9.5% highlighted 1 off graph | | Planar groups: 100.0% within limits 0.0% highlighted | | | +----------------------------------------------------------------------------+ + May be worth investigating further. * Worth investigating further. MODEL 2 +----------<<< P R O C H E C K S U M M A R Y >>>----------+ | | | input_atom_only.pdb 2.5 859 residues | | | *| Ramachandran plot: 64.7% core 28.0% allow 4.6% gener 2.7% disall | | | *| All Ramachandrans: 147 labelled residues (out of 825) | *| Chi1-chi2 plots: 16 labelled residues (out of 472) | +| Main-chain params: 4 better 0 inside 2 worse | | Side-chain params: 5 better 0 inside 0 worse | | | *| Residue properties: Max.deviation: 9.3 Bad contacts: 0 | *| Bond len/angle: 7.1 Morris et al class: 3 2 2 | *| 5 cis-peptides | +| G-factors Dihedrals: -0.90 Covalent: -0.13 Overall: -0.57 | | | | M/c bond lengths:100.0% within limits 0.0% highlighted | | M/c bond angles: 90.2% within limits 9.8% highlighted | *| Planar groups: 57.1% within limits 42.9% highlighted 69 off graph | | | +----------------------------------------------------------------------------+ + May be worth investigating further. * Worth investigating further. S.Harikrishna

1 0

loop error
by albert 19 Feb '12

19 Feb '12

Hello: I am trying to generate loop models with loop protocol in the latest Modeller verison. It only produced 8 models and stopped, and it said the following: File "loop.py", line 41, in <module> a.make() File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 190, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 208, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 131, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 164, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 180, in _process_event task = obj.task_results() File "/usr/lib64/python2.7/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 89, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 130, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: <type 'ValueError'>: GA341______E> Sequence identity -999.000 out of range - must be between 0 and 100. Seq. ID is read from the model.seq_id variable, which is obtained automatically from the REMARK lines of MODELLER-produced PDB files from <Slave on localhost>

2 1

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()

2 1

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

1 0

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

2 3

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

2 1

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

2 1