November 2011 - modeller_usage

Enc: Error with import os
by Bruno Madio 30 Nov '11

30 Nov '11

Dear Modeller, When I try to do anything with modeller9.10, an error menssage occurs with "C:\Program Files (x86)\Modeller9.10\modlib\modeller\__init__.py" line 51 and I can´t import "os" from "C:\Program Files (x86)\lib\os.py" line 106. Please, could you help me fix this bug? I have read the release notes, but I still could not fix the error. Could you teach me step by step? All the best, Bruno Madio

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 148
by Ashish Runthala 30 Nov '11

30 Nov '11

Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!) Sorry to say sir benn, but MODELLER do refine the models to some extent if the mutual orientation of individual domains in a multi-domain structure or the initial models's topology is correct and parallel to the actual native structure. But all this fun of pulling the models closer to native state works well only when the correct model decoy is correctly selected for. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, November 30, 2011 7:32:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 148 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Refine part of an existing model (Modeller Caretaker) 2. Is there any Modeller Script to refine unaligned loop chunks (Ashish Runthala) 3. Enc: Error with import os (Bruno Madio) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 Nov 2011 12:22:25 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Refine part of an existing model To: flavio seixas <oivalf_nix(a)yahoo.com>, Modeller Queries <modeller_usage(a)salilab.org> Message-ID: <4ED53F01.2020907(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/29/2011 03:03 AM, flavio seixas wrote: > I was studing Modeller manual and I am not sure if there is a routine > in modeller that can refine only part of an existin model, like loop > refinement do. Just build a new comparative model using the regular automodel class, using your original model as the template. Use a simple alignment containing two copies of the model sequence. Override select_atoms() as per the example at http://salilab.org/modeller/9.10/manual/node23.html to define the region to refine. Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!) > However, the region that I am interested to refine is > not a loop. Because of this, I can not use loop refinement in helical > segments, even though a region of three residues. Loop refinement can be used for any region without a template. The protein can adopt any secondary structure, including an alpha helix. But yes, typically loop refinement will give you coil structures. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Wed, 30 Nov 2011 15:02:09 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] Is there any Modeller Script to refine unaligned loop chunks To: modeller <modeller_usage(a)salilab.org> Message-ID: <10902351.27461322645529168.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem. Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region. SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE. Thanks a lot, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 3 Date: Wed, 30 Nov 2011 05:48:11 -0800 (PST) From: Bruno Madio <brunomadio(a)yahoo.com.br> Subject: [modeller_usage] Enc: Error with import os To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Message-ID: <1322660891.50858.YahooMailNeo(a)web45310.mail.sp1.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear Modeller, When I try to do anything with modeller9.10, an error menssage occurs with "C:\Program Files (x86)\Modeller9.10\modlib\modeller\__init__.py" line 51 and?I can?t ?import "os" from "C:\Program Files (x86)\lib\os.py" line 106. Please, could you help me fix this bug? I have read the release notes, but I still could not fix the error. Could you teach me step by step? All the best, Bruno Madio

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Is there any Modeller Script to refine unaligned loop chunks
by Ashish Runthala 30 Nov '11

30 Nov '11

Dear Modellers, Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem. Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region. SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE. Thanks a lot, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Refine part of an existing model
by flavio seixas 29 Nov '11

29 Nov '11

Hi Modellers I generated a 1000 models of a protein using Modeller. The best one shows 3 residues in disallowed regions of Ramachandram plot. I want to refine only regions around those 3 residues which are in helical segments. The script I am using in is not working. Unfortunately I am not familiar with pyton script. The error message and script file are as follow: File "model-segment.py", line 35 a = MyModel(env, inimodel='182.pdb', sequence='Seq-target') ^ SyntaxError: invalid syntax --------------------------------------------------------------------------- from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 env.io.hetatm = True class MyModel(automodel): def select_atoms(self): # Select residues (PDB numbering) return selection(self.residue_range('72:A', '75:A'), (self.residue_range('165:A', '167:A'), (self.residue_range('199:A', '201:A')) # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, inimodel='182.pdb', sequence='Seq-target') a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling Could someone help me in this regard? Thanks for any help. Flavio

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sequence identity
by Полякова Марина 28 Nov '11

28 Nov '11

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Loop modelling
by Bishwajit Das 23 Nov '11

23 Nov '11

Dear modellers when i use automodel class in modelling a protein then is it necessary to run another loop model program?? please help me about this . -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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loop modelling
by Bishwajit Das 23 Nov '11

23 Nov '11

Dear modellers when i use automodel class in modelling a protein then is it necessary to run another loop model program?? please help me about this . -- *BISHWAJIT DAS* *+91-9433237920* KOLKATA

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Loop Model ranking
by flavio seixas 23 Nov '11

23 Nov '11

Hi Ben First of all I would like to apologise for a so basic question. However, I am not a pyton expert and do not have another one to ask here. I run the loop.py scritp to generate 200 models. However, my attempt to rank the models by DOPE score fails. I am using the script below: ############################################ from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Two residue ranges (both will be refined simultaneously) return selection(self.residue_range('23:A', '25:A'), self.residue_range('73:A', '75:A')) m = MyLoop(env, inimodel='Modeloutput23.pdb', sequence='Target1', loop_assess_methods=(assess.DOPE, assess.GA341)) m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 200 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.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 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) ############################## I realise that "loop assess methods" could not be the same sintax for "model assess methods", but I do not know how to correct it in the script Could you give me any help? Thanks in advance, Flavio

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error in align codes
by si yang 17 Nov '11

17 Nov '11

Hi, i am Yang here.. I try to build a model by using basic tutorial, that begin with only protein sequence, to look for potential templates. However, i have encountered a problem during build_profile.py loading, it generate problem as below: Protein specified in ALIGN_CODES<i>, was not found in the alignment file;ALIGN_CODES< 1>= ALL The alignment file i saved in plain text format, with suffix .ali (bleg1_2439.ali), is that affected the reading by modeller? I don't specified the templates are used, so just follow the python file from basic example, the only thing i change, is only the align file that attached above.. Your feedback is important and appreciated.. Thank you

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Protein-DNA loop model
by Rubben Torella 17 Nov '11

17 Nov '11

Hi all, I used Modeller in the past to create small loops from scratch. Now I have a protein-DNA complex, and I have to build and model 4 loops of my protein. My first problem is that MODELLER does not support DNA, so I have to strip the DNA from the PDB and use the protein alone. Considering the problem that I have to "paste" the DNA to the modelled structure, I use the options *a.md_level= None* to keep the rest of the protein fixed and the option * a.loop.md_level* to model the loops. Now, these two commands work on three of the 4 loops, but I have another problem now: I have a very long loop to build (35 aa) and using these two commands, MODELLER create a very strange hairpin loop to connect these two positions. I know which will be the correct structure of this loop because I have a similar protein that present this loop, and the modelling is wrong. Finally, if I don't usage a.md_level=None, MODELLER builds a very good loop, but all the protein is in a complete different position with respect of the starting one. Any suggestion? Best regards Rubben -- PhD Student, Prof.Glen Group University of Cambridge, Unilever Center, Lensfield Road CB2 1EW Cambridge, Cambridgeshire, United Kingdom University Phone : +44 (0)1223 336432 Cell Phone: +44 (0)774 3358973

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