April 2024 - modeller_usage

_modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables.
by Rana Rehan Khalid 06 May '24

06 May '24

Dear Modeller Users, I am currently attempting to generate various mutant models using the MutantBuilder script available at https://github.com/eved1018/MutantBuilder. I have installed Modeller10.5 for this purpose. However, I am encountering the following issue: python3 MutantBuilder.py -pdb complex.pdb -c B Traceback (most recent call last): File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 372, in <module> main() File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 368, in main model(pdb, mutants, chain, mutant_name, outfolder) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 188, in HomologyModel mutant_pdb = autoModelPDB(pdb, aln ) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 204, in autoModelPDB a.make() File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 638, in homcsr self.mkhomcsr(Selection(self), aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 716, in mkhomcsr self.build_charmm_restraints(atmsel, rsr, aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 678, in build_charmm_restraints rsr.make(atmsel, aln=aln, restraint_type=type+'_dihedral', File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/restraints.py", line 156, in make return func(self.__mdl.modpt, edat.modpt, aln.modpt, io.modpt, _modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables. Could someone please assist me in resolving this problem? Your help would be greatly appreciated. Best Wishes Rehan

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my automodel run well serial, but molpdf is inmediatly exceeded when run in parallel
by Mario Bianchet 16 Apr '24

16 Apr '24

Hello All The script below exceeds molpdf limits immediately when run this automodel job on parallel, but run starts with a low molpdf and ends well when commenting the line "a.use_parallel_job(j)" Any hint of how to solve will be appreciate? Mario from modelito import MyModel from modeller.parallel import * icycle=50 log.minimal() # request minimal output env = Environ() # create a new MODELLER environment to build this model in icycle=str(int(icycle)+1) # directories for input atom files env.io.atom_files_directory = ['.', 'trajs/'] # Give less weight to all soft-sphere restraints: env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) # Very thorough VTFM optimization: j = Job() for i in range(1): j.append(local_slave()) # Comparative modeling by the AutoModel class env.io.hetatm=True a = MyModel(env, alnfile = 'test.ali', # alignment filename knowns = ('ro','odo'), # codes of the templates sequence = 'TEST') # code of the target a.starting_model= int(icycle) # index of the first model a.ending_model = int(icycle)+ 0 # index of the last model # (determines how many models to calculate) a.library_schedule = autosched.slow #a.restraints.write(file='restraints.rsr') # Thorough MD optimization: a.md_level = refine.slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.use_parallel_job(j) a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # do the actual comparative modeling

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Re: About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by Modeller Caretaker 16 Apr '24

16 Apr '24

On 4/16/24 8:22 AM, c00jsw00 wrote: > thanks for your help. When I use win 11 (anaconda powershell) to run a > simple python input and got the error. ... > File "D:\conda\Library\modeller\modlib\modeller\util\logger.py", line 8, > in Logger > _header = _modeller.mod_header_get() > ^^^^^^^^^^^^^^^^^^^^^^^^^^ > UnicodeDecodeError: 'utf-8' codec can't decode byte 0xaa in position > 957: invalid start byte Ah, I see the problem. It is trying to print the start of the Modeller log file, which has information on the Modeller version and environment. Position 957 is about where your computer name is. We assume that name is valid ASCII or UTF8 (and nobody's reported this error before!) but I suppose it doesn't have to be, particularly in non-Western locales. We'll fix this issue for the next Modeller release. In the meantime you could work around it in one of two ways: 1. Change your computer name in Control Panel to something containing only plain ASCII (e.g. try "XXX") and reboot. or 2. Edit logger.py in your Modeller installation, i.e. D:\conda\Library\modeller\modlib\modeller\util\logger.py and change line 8 from _header = _modeller.mod_header_get() to _header = ' ' Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by c00jsw00＠kmu.edu.tw 15 Apr '24

15 Apr '24

Dear all, When I use conda to install modller 10.4 or 10.5, I used the python (3.9) to run a simple command (from modeller import *). Then I got the error (UnicodeDecodeError: 'utf-8' codec can't decode...) . Could you tell me how to overcome it ? THX YT

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Perodic boundary condition?
by Qizan Chen 05 Apr '24

05 Apr '24

Can the Modeller take periodic boundary conditions into account during modeling? I aim to construct a condensed model, but currently, unwarping the protein to the Modeller and then warping it back leads to incorrect overlaps of side chains. I noticed that symmetry constraints can be added, but my original system is already large, and adding additional images causes crashes.

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