- modeller_usage - salilab.org

Regarding Iterative Sequence Alignment
by Ashish Runthala 24 Feb '11

24 Feb '11

Dear Modellers, I want to generate iterative sequence alignment of Templates before being integrated with the target sequence. How to use salign for optimal iterative alignment only based on sequences, with no consideration of overhang folds. Thanks Ashish Ashish Runthala Lecturer, Structural Biology Cell, Biological Sciences Group, BITS Pilani, Rajasthan - INDIA

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bad occupancy from loop refinement
by albert 22 Feb '11

22 Feb '11

Hello: I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1. here is some list, can you tell me why? THX -----------------------------Loop refinement---------------------------------------------- EXPDTA THEORETICAL MODEL, MODELLER 9v8 2011/02/18 21:54:47 REMARK 6 MODELLER OBJECTIVE FUNCTION: -11.8879 ATOM 1 N SER A 1 53.405 4.206 73.937 59.86 59.86 ATOM 2 CA SER A 1 54.091 5.156 73.036 59.86 59.86 ATOM 3 CB SER A 1 53.358 5.255 71.687 59.86 59.86 ATOM 4 OG SER A 1 53.443 4.020 70.992 59.86 59.86 ATOM 5 C SER A 1 54.148 6.519 73.639 59.86 59.86 ATOM 6 O SER A 1 54.469 6.679 74.816 59.86 59.86 ATOM 7 N ALA A 2 53.848 7.547 72.824 39.90 39.90 ATOM 8 CA ALA A 2 53.862 8.892 73.313 39.90 39.90

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loop model error
by albert 18 Feb '11

18 Feb '11

Hi: I am using model loop based on initial PDB files, but there is a error: Traceback (most recent call last): File "model.py", line 41, in ? a.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 36, in make automodel.make(self, exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 411, in homcsr aln = self.read_alignment() File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 401, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/lib64/python2.4/site-packages/modeller/alignment.py", line 81, in append allow_alternates) IOError: openf______E> Cannot open file : No such file or directory

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how seed influence the Modeller results?
by albert 18 Feb '11

18 Feb '11

Hi: I've got a question about how seed influence the Modeller results? If I start from the same seed in the same computer, does it means it should get the same results? If two job both start from random seed or different seeds, they will get different results, and those results is comparable with running model building jobs with doubled model number building? THX

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plot_profiles.py errors
by hari krishna 18 Feb '11

18 Feb '11

I installed MatPlotLib 2.6v. (python2.6) Still it is showing me the error: File "plot_profiles.py", line 1, in ? import pylab Importerror: No module named pylab Please help me to over come this problem. *Thanks in advance..*

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modeller and win64
by Igor Dvortsov 17 Feb '11

17 Feb '11

so the subj. could authors of modeller build x64 version of _modeller.pyd? kind regards, Igor

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Protein - DNA Modelling
by Koushik A C 17 Feb '11

17 Feb '11

Hi, I wanna perform a protein - DNA modelling. But I don't know how to proceed. Can anyone help me with any tutorial or steps? --Kaushik

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 33
by Ashish Runthala 16 Feb '11

16 Feb '11

You remove the chain identifier from both align2d.py and model_multiple.py (Or, whatever you are using) This is how i did it in one of the run. Thus, Align2d.py becomes mdl = model(env, file='Run2BestModel', model_segment=('1','292')) #No ChainID is here with model residue positions aln.append_model(mdl, align_codes='Run2BestModel', atom_files='Run2BestModel') So, Model_multiple.py will be a = automodel(env, alnfile = 'alignment.ali', knowns = ('Run2BestModel'), sequence = 'target', assess_methods=(assess.DOPE, assess.GA341,assess.normalized_dope)) a.starting_model= 1 a.ending_model = 1000 a.make() Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA

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mutiple CPU error
by albert 16 Feb '11

16 Feb '11

Hi I try to build model with my own constrain(beta sheet) with multiple CPU, but it said: ----------------log-------------------- raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'MyModel' from <Slave on localhost> I ues the following script for multiple CPU: -------------script------------------------ 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()) env = environ() log.verbose() ---------------------------------------------- THX

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initial model error
by albert 16 Feb '11

16 Feb '11

Hi: I would like to build a model staring from my own model. but it didn't work, it is said: -------log-------------- _modeller.ModellerError: rdpdb___303E> 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 " ", chain " "; atom file name: init.pdb -------------------------- In fact in the alignment file I already add something like this: -------------------align---------------------------- >P1;seq sequence:seq: : : : ::: 0.00: 0.00 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >P1;init structureX:init.pdb:1 :A: :A:::-1.00:-1.00 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >P1;temp structureX:temp.pdb:1 :A: :A:::-1.00:-1.00 aaaaaaaaaaaaaaaaaabbbbbbbbbbbb ----------script------------------------------------- class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('146:', '150:'))) rsr.add(secondary_structure.strand(self.residue_range('156:', '161:'))) a = MyModel(env, alnfile='mult.ali', knowns=('tempA'), sequence='my', inifile = 'init.pdb') a.starting_model = 1 a.ending_model = 2 ---------------------------------------------------------------------------- the seq and init share the same sequences. The starting model init.pdb contains a china named A. could you give me some advices? THX

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