January 2010 - modeller_usage

How can I get restraint energies of initial structure without building a model.
by Lee, Jinhyuk 28 Jan '10

28 Jan '10

Dear All, The following one after the main text is my script to get energies. I put my restraint file (L001.rsr) and my initial structure (init.pdb). I want to see the energies on initial structure without building (energy minimization) a model so that I include "max_var_iterations=0" in the script. However, Modeller complained like that. > Summary of failed models: T0388.B99990001.pdb ddihedr_262E> Central bond too short: 0.0000 Is there any other scripts to do the same job? Thanks alot ----Script from modeller.automodel import * # Load the automodel class log.verbose() env = environ() env.io.atom_files_directory = './' templates=('3gb1') a = automodel(env,alnfile = 'L001.ali',knowns= templates,sequence='L001',inifile='init.pdb',csrfile = 'L001.rsr') a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.max_molpdf=10000000000000.0 a.max_var_iterations=0 a.make() # do homology modelling

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Cutoff for distance restraints
by Armin Meier 28 Jan '10

28 Jan '10

Hi, where can I find the maximal length of CACA, NO, SCMC and SCSC distance, for which restraints are yet generated by Modeller, i.e. there must be a cutoff for e.g. CACA distances, which - when exceeded - determines that no restraint is generated. What are these cutoffs? Thanks a lot Armin Meier

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Dope score
by vidhya vasanth 27 Jan '10

27 Jan '10

Hello, In modeling, the best model can be judged by either low dope score or low molpdf. But, what is a dope score? Why the best model is selected based on low dope score?? Thanks RegardsVidhya The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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how to cite Modeller9v7?
by leuven 23 Jan '10

23 Jan '10

I am going to publish a paper and I am wondering how to cite Modeller9v7? thanks

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Using modeller for checking metagenomic distant homologs
by Ben Temperton 22 Jan '10

22 Jan '10

Hi there, I am currently writing a pipeline to identify distant homologs of genes in metagenomic samples using HMMER 3.0 and hmm models of conserved domains from Pfam. Once I have identified putative homologs, I would like to verify that these homologs are indeed homologs by threading them onto a known protein structure and evaluating whether the threading was successful. Given I'm very new to protein threading, is Modeller an ideal tool to use for this application? Many thanks, Ben Temperton

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Question about chi dihedral angle cubic spline restraint
by Lee, Jinhyuk 22 Jan '10

22 Jan '10

Dear all, I have a question about chi dihedral angle in rsr (restraint) file. The following is one of chi1 dihedral angles. R 10 22 3 14 4 28 0 1 2 3 4 1.0000 -3.1416 3.1584 0.3000 0.1072 -1.8388 0.3519 0.5736 1.8270 4.1095 4.6770 1.6637 0.1167 0.0925 1.5911 4.6125 7.2224 6.4874 3.6210 1.5701 0.8375 1.4232 3.3272 6.1649 5.4708 2.8728 1.0891 0.3370 I think that the 14th and 15th columns (-3.1416 and 3.1584) represent the low and high points, respectively. The chi angle should be periodic from -pi to pi radians, but two values do not agree with pi and -pi. When I generated the spline function using these data and the values at pi and -pi seems to be disagreement. Is there any reason of using -3.1416 and 3.1584 not pi and -pi? Thanks, -- Jinhyuk

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muliplay cpu
by Knut J Bjuland 21 Jan '10

21 Jan '10

How do I use multiple cpu when doing loop which I have shown in a script below. I am trying to use several cpus to get a faster build of a model. Knut J rom modeller import * from modeller.automodel import * from modeller.parallel import * env = environ() j= job() j.append(local_slave()) #cpu 1 j.append(local_slave()) #cpu 2 j.append(local_slave()) #cpu 3 j.append(local_slave()) #cpu 3 j.start() class Model(automodel): def select_atoms(self): return selection(self.residue_range('1:','180:')) a=Model(env,alnfile='hNaa10p.ali', knowns='2OB0', sequence='hnaa10', assess_methods=assess.DOPE) a.starting_model=1 a.ending_model=200 a.use_parallel_job(j) a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key])

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good book about modeller.
by Knut J Bjuland 18 Jan '10

18 Jan '10

I am looking for a good book about molecular modellering, and in particular a good book about modeller. Knut J

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Re: [modeller_usage] Modeling a larger protein in several steps
by nornik 17 Jan '10

17 Jan '10

I noticed that the alignment made no sense at all so I resend the message with a new one with mono space characters and hope it will be easier: Hello I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template ----BBBBSBBBBBBB--------------------------------------------------- template2 ----------CCCCCCCCCSCCCCC------------------------------------------ template3 ----------------------------------DDDDDSDDDDDDDSDDDDDD------------- template4 ----------------------------------------------------------EEEESEEEE template5 sulfur bridge sulfur bridge sulfur bridge Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "deletions" with the other four templates and still maintain the sulfur bridges. Any other suggestions are of course also welcome in trying to solve this problem. Thank you

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Modeling a larger protein in several steps
by nornik 13 Jan '10

13 Jan '10

Hello I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this MMMMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMMMMMMMMMMMMMM Model AAAAAAAAAAA---------------------------AAAAAAAAAAAAAAAAAAAAA------------------------AAAAAAAAASAA------------------------------- core template --------------BBBBSBBBBBBB------------------------------------------------------------------------------------------------------------------------- template2 ---------------------------CCCCCCCCCSCCCCC----------------------------------------------------------------------------------------------------- template3 -------------------------------------------------------------------------DDDDDSDDDDDDDDDSDDDDDD-------------------------------------------- template4 ---------------------------------------------------------------------------------------------------------------------EEEEEEEEEEEEEEEEESEEEEEEE template5 __sulfur bridge___ _sulfur bridge_ ___sulfur bridge___ Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "deletions" with the other four templates and still maintain the sulfur bridges. Any other suggestions are of course also welcome in trying to solve this problem. Thank you Niklas

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