- modeller_usage - salilab.org

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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question about Modeling with cryo-EM compare.
by Knut J Bjuland 12 Jan '10

12 Jan '10

When you read the second part of this tutorial at http://salilab.org/modeller/ncmi_2008/select.html. How do you read this table, or is there any function in modeller that use the table and output sequence identity. Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1b8pA @11y7tA @11civA @25mdhA @27mdhA @23d5tA @21smkA @2 1b8pA @1 327 201 146 152 152 249 50 1y7tA @1 61 327 158 170 160 210 58 1civA @2 45 48 374 140 304 148 55 5mdhA @2 46 52 42 333 140 164 58 7mdhA @2 46 49 87 42 351 148 50 3d5tA @2 78 65 46 51 46 321 50 1smkA @2 16 19 18 19 16 16 313 I am not able to read the this table manually and I can not see how I can extract sequence_identity from it. Best regards Knut J _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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mutipule cpu run errors.
by leuven 12 Jan '10

12 Jan '10

hello all: I try to use multiple cpu with modeller, but it fails, here is my srcipts: # Example of changing the default optmization schedule from modeller import * from modeller.automodel import * from modeller.parallel import * # Load the parallel class, to use multiple processors j = job("/usr/lib/modeller9v7/bin/modslave.py") j.append(local_slave()) # 1 Processor j.append(local_slave()) # 2 Processors And here is the error: /soft/python/lib/python2.5/site-packages/modeller/__init__.py:69: RuntimeWarning: Python C API version mismatch for module _modeller: This Python has API version 1013, module _modeller has version 1012. import _modeller /soft/python/lib/python2.5/site-packages/modeller/__init__.py:69: RuntimeWarning: Python C API version mismatch for module swig_runtime_data4: This Python has API version 1013, module swig_runtime_data4 has version 1012. import _modeller

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how to build mutations with different resiudes to different target residues?
by leuven 11 Jan '10

11 Jan '10

I want to build mutation model with 5 residues. The no. of this residues is : 16, 42 56, 88, 152, and they are mutated into different residues. How to achieve this? I found something at http://salilab.org/modeller/manual/node234.html, but I don't think this example is suitable for my situation. Thank you very much.

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