- modeller_usage - salilab.org

Optimization and modelling
by Piyush Diyora 24 Jun '10

24 Jun '10

I followed the steps mentioned by John W. "(To find a native like structure I created 100 models for 5 different template combinations with and without loop modelling and with and without MD refinement, and I found that no loop modelling and no MD refinement gave me the best models. I took my 5-10 best models as ranked by dope and the objective function followed by PROsa analysis. Then I further analyzed the 5 or so best via procheck. IMO brute force and sheer numbers are the best way to determine emperically what combinations of settings will work best for you. I would definitely try no loop model and no MD and always do 100 models minimum. Cheers.") - John W., After choosing the best models, based on the gap (where no template structure was available), i performed slow loop optimisation. As I am new to modelling, I don't know how can I optimise my model more accurately http://sites.google.com/site/piyushdiyora/ The above link has an image before and after optimisation. Should i optimize other parts of he model, because there are several high peaks. Second question is, I am working on Dos1 protein from Fission Yeast. Sequence blast in Protein data bank provided 75 results. Out of these none of them were completely identical, but only part (fragment around 80 - 120 amino acid long) of the Dos1 sequence was identical to the (fragment) reference templates. Similarly other part was identical to other reference template. Based on such analysis, I went through all 75 protein 1) extracted the part of the sequence from reference template and then aligned with the Dos1 protein (http://sites.google.com/site/piyushdiyora/home/second-page) My question is 1) As these fragments are from different protein having different 3d structure, HOW RELIABLE WILL BE MY PROTEIN 3D STRUCTURE? 2) If I want to build a model based on the reference template (created by joining all the fragments), how should i do it? I dont know how to manually modify the sequence file (which will be used by modeller) Thank you in advance :)

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Loop Refinement - Clustering necessary?
by Jan H. Löhr 22 Jun '10

22 Jun '10

Dear Modeller users, according to posts in this mailing list as well as the background information to ModLoop, the best loop-model is chosen by lowest pseudo-energy score (http://modbase.compbio.ucsf.edu/modloop/ - Fiser's and Sali's papers cited at the bottom of the page). However, the tutorial of Modeller indicates that "it is important to note that a most accurate approach to loop refinement requires the modeling of hundreds of independent conformations and their clustering to select the most representative structures of the loop" http://www.salilab.org/modeller/tutorial/advanced.html) I have been comparing different loop-models generated by loop.model for a selected region of a pdb-file and I am tempted to simply choose the best DOPE-HR-scoring model. Yet the clustering idea does makes sense. So far, the greatest cluster of models often contains (one of) the best scoring model(s), but not in every case. My question is therefore: Should the best model be chosen, or should the best model of the greatest cluster be chosen? I wonder about your opinions regarding this issue. In case anyone is voting for the clustering method: What method is easily suitable for clustering - unfortunately, the loop.model-class does not seem to have an integrated clustering option, does it? Regards Jan Jan H. Löhr Univ. Hamburg, Germany

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Using my own initial structure to model a loop
by Thomas Evangelidis 16 Jun '10

16 Jun '10

I was looking at : http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel and was wondering if it's right to pass a loop fragment generated de novo into automodel with the inifile parameter. Is it the same as using it as a template in the alignment (that's what I do so far)? If yes, can I define multiple infiles to model multiple loops of my protein whilst doing homology modeling for the rest of it?

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Modeling with multiple templates
by sdh 16 Jun '10

16 Jun '10

Hello all! I want to model a big fibrous protein using several templates. The templates do not overlap (gap is no longer then 1-3 residues) or overlap over few residues. I found the following sentence in the FAQ: "If no additional information is available about the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains when the overlap between A and B is non-existing or short. To obtain satisfactory relative orientation of modeled domains in such cases, orient the two template structures appropriately before the modeling." My questions are: how precisely the templates have to be oriented? Would be cursory placing enough? How can I order the templates by using some simple constraints instead of orienting the templates? Thanks for help, sdh

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Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 88
by John W 15 Jun '10

15 Jun '10

I can't address your own results, but I can tell you my experience: To find a native like structure I created 100 models for 5 different template combinations with and without loop modelling and with and without MD refinement, and I found that no loop modelling and no MD refinement gave me the best models. I took my 5-10 best models as ranked by dope and the objective function and then submitted them to PROsa. Then I further analyzed the 5 or so best via procheck. IMO brute force and sheer numbers are the best way to determine emperically what combinations of settings will work best for you. I would definitely try no loop model and no MD and always do 100 models minimum. Cheers. --- On Tue, 6/15/10, modeller_usage-request(a)salilab.org <modeller_usage-request(a)salilab.org> wrote: From: modeller_usage-request(a)salilab.org <modeller_usage-request(a)salilab.org> Subject: modeller_usage Digest, Vol 9, Issue 88 To: modeller_usage(a)salilab.org Date: Tuesday, June 15, 2010, 8:25 AM 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. structure refinement and loop optimization protocol (Thomas Evangelidis) 2. Using my own initial structure to model a loop (Thomas Evangelidis) ---------------------------------------------------------------------- Message: 1 Date: Tue, 15 Jun 2010 02:29:37 +0100 From: Thomas Evangelidis <tevang3(a)gmail.com> Subject: [modeller_usage] structure refinement and loop optimization protocol To: modeller_usage(a)salilab.org Message-ID: <AANLkTil1lD1Yf9cWtV5O1ID9kxv7QZkzaDcz3b4n0iBo(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Modellers, I've read previous posts on the same topic and concluded that it is better to generate multiple models with moderate refinement and loop optimization level, rather that a few with very thorough parameterization. I've also noticed myself that with the thorough parameterization parts of the secondary structure are distorted. I have concluded about the optimum alignment after a lot of experimentation and would like to set up a very effective optimization process. However I'm not sure about the output files. My code looks like this: a = MyLoopModel(env, alnfile=alignment, > knowns=known_templates, > assess_methods=(assess.DOPEHR,assess.normalized_dope), > sequence='target') > a.starting_model = 1 > a.ending_model = 2 > # Normal VTFM model optimization: > a.library_schedule = autosched.normal > a.max_var_iterations = 200 ## 200 by default > # Very thorough MD model optimization: > a.md_level = refine.slow > a.repeat_optimization = 1 > > a.loop.starting_model = 1 # First loop model > a.loop.ending_model = 5 # Last loop model > a.loop.md_level = refine.slow # Loop model refinement > level > Which generates the following pdb files: target.B99990001.pdb target.B99990002.pdb target.BL00040002.pdb > target.IL00000001.pdb target.IL00000002.pdb > I thought the above should perform model refinement twice and write 5 different conformations (loop optimization) for each. So my questions are the following: 1) Can you explain what's happening with the .pdb files? 2) I 'd like to ask your opinion about the most effective way to find a near-native protein conformation in low sequence identity levels. How should the parameters shown above be set? I don't care if it's running a day or so as long as I get good results. 3) I also attempted to cluster the models with a.cluster(cluster_cut=1.5), which generated a representative structure with the parts of the protein that remained similar in most of the models but without the variable parts (files cluster.ini and cluster.opt). Does it make sense to select the model that is closer to that consensus structure? If yes is there a way to do it with Modeller? I know it can been found with Maxcluster program. Or alternatively, do you reckon it is better to select the based model based on the normalized DOPE z-score? Hope to get some answers on these question cause I've been strangling to find the best refinement/optimization protocol for several weeks. thanks, Thomas

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structural alignment of models respect template(s)
by David Rodríguez 12 Jun '10

12 Jun '10

Hi, I am interested in making a 3D structural alignment of the resulting models with their template(s). I have included the "a.final_malign3d = True" line in the script as stated in the manual, and the *_fit.pdb files were generated. However, none of the models are correctly aligned to the template. I wonder if anyone knows a successful way to align the models with just one modeling script. I could provide inputs and outputs if necessary. Thanks in advance. Best regards, -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) E-mail: david.rodriguez.diaz at usc dot e

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Fwd: SALIGN
by Piyush Diyora 12 Jun '10

12 Jun '10

> HI, > I performed multiple sequence alignment using salign. When I analysed the result output (.pap output), there was some improper alignment at 400th position. Because of that, entire alignment after that error was improper. How can I improve the alignment and what is the reason for such mistakes. > > I have attached the file containing sequence of the protein, salign code and the pap output file.

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Modeling a dimer
by Konstantin A. Odynets 10 Jun '10

10 Jun '10

Dear Modeller users, my templates are a homodimer of the first domain and a monomer of the second domain, and the target protein is a homodimer. Both domains are linked by 17 aa flexible regions without templates. How could I do such task in Modeller 9.8? >P1;1n3l structureX:1n3l:4:A:342:B:hstyrrs-N_2x342:homo sapiens:1.18:0.18 -AAAAAAAAAA-AAAAAA-------/-BBBBBBBBBB-BBBBBB-------* >P1;1ntg structureX:1ntg:2:A:170:A:hstyrrs-C_1x169:homo sapiens:2.21:0.251 -------------------CCCCCC* >P1;hstyrrs sequence:hstyrrs:1:A:528:B:hstyrrs_2x528:homo sapiens:2.00:-1.00 AAAAAAAAAAAAAAAAAALCCCCCC/BBBBBBBBBBBBBBBBBBLCCCCCC* Thank you in advance for your help. Best regards, Konstantin. --- Konstantin A. Odynets Institute of Molecular Biology and Genetics Academician Zabolotny street, 150, Kyiv, Ukraine E-mail: odynets(a)imbg.org.ua

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Parallel Python (socket.error: (111, 'Connection refused')
by Laurence Cooke 10 Jun '10

10 Jun '10

Hello, I have password-less ssh and rsh (I've tried both; same "Connection refused" error). My home directory is NFS mounted to all slave machines. I successfully ran parallel python with Modeller9v7 in the past with this setup but now since updating to Mod9v8 I'm not able to run the same scripts. It's been a while since I've used Modeller so I'm not sure if the problem is due to updating Modeller or changes that might have occurred in the computer configurations. Again ssh and rsh work seamlessly between all nodes without passwords. Also: I'm able to run the scripts using 'local_slave()'. I updated to Modeller9v8 on all machines. All nodes are correctly listed in the /etc/hosts files on all machines. We do run other software apps that require password-less ssh and they are working well. Nodes are quad core processors. Finally: I included below the code I'm running as well as the Modeller output in the *.slave files. Any help would be greatly appreciated. Regards, Laurence Cooke Arizona Cancer Center Tucson, Arizona ****************************************** Start Parallel Task Remote file (one node) ****************************************** from modeller import * from modeller.parallel import * from buildmodeltask import BuildModelTask log.minimal() j = job() j.append(ssh_slave('slave1', ssh_command='ssh')) j.append(ssh_slave('slave1', ssh_command='ssh')) j.append(ssh_slave('slave1', ssh_command='ssh')) j.append(ssh_slave('slave1', ssh_command='ssh')) j.queue_task(BuildModelTask('alignment_1.ali','pdb','sequence_1')) j.queue_task(BuildModelTask('alignment_2.ali','pdb','sequence_2')) j.queue_task(BuildModelTask('alignment_3.ali','pdb','sequence_3')) j.queue_task(BuildModelTask('alignment_4.ali','pdb','sequence_4')) results = j.run_all_tasks() print "Done: ", results ***************************** BuildModelTask file ****************************** import random from modeller import * from modeller.parallel import task from modeller.automodel import * class BuildModelTask(task): def run(self,ali,pdb,unknown): env = environ(rand_seed=(random.randint(2,50000)*-1)) env.io.hetatm = True a = automodel(env, alnfile=ali, knowns=pdb, sequence=unknown, assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 250 a.make() ********************************* *.slave0-4 files ********************************* Slave startup: connect to master at 127.0.0.1:59941:0:LMTRWVLB Traceback (most recent call last): File "/usr/lib/modeller9v8/bin/modslave.py", line 27, in ? slaveloop(sys.argv[2]) File "/usr/lib/python2.4/site-packages/modeller/parallel/slaveloop.py", line 57, in slaveloop master.connect_back(host, port, identifier) File "/usr/lib/python2.4/site-packages/modeller/parallel/slave_communicator.py", line 15, in connect_back s.connect((host, port)) File "<string>", line 1, in connect socket.error: (111, 'Connection refused') DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail.

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how to obtain the results from assess_methods from automodel() object
by Thomas Evangelidis 10 Jun '10

10 Jun '10

Dear Modeller Caretaker, I use assess_methods=(assess.DOPEHR,assess.normalized_dope) within the automodel constructor to evaluate thousands of models during structure prediction. As you see it becomes very difficult to trace these values within the log files, and assign the scores to the correct files and alignments. Is there any easier way to obtain these values from the instance of automodel(), i.e. ... a = MyModel(env, alnfile=alignment, knowns=known_templates, assess_methods=(assess.DOPEHR, assess.normalized_dope), sequence='target') .... a.make() dopehr_score = a.get_dopehr(modelNo) ## something like this thanks in advance, Thomas

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