- modeller_usage - salilab.org

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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program to manually edit the structure
by Thomas Evangelidis 07 Jun '10

07 Jun '10

Dear Modellers, are you aware of any commercial free software that allows you to flip side-chains manually and correct bad torsion angles?

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Re: [modeller_usage] Running GA341 Assessment
by David Tiberi 03 Jun '10

03 Jun '10

Hi, I have tried to implement this assessment criteria to evaluate some of my homology models. However, after having run all of the scripts, I keep ending up with a value of 0.0000. Attached to this e-mail I have included the outputs I received while trying to run the assessment. Could you please lend some insight on this matter. Thank you in advance, D.T

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Modelling missing residues
by Omar Davulcu 03 Jun '10

03 Jun '10

Hi everyone, I have a crystal structure for an enzyme (1M80) that is missing a loop, residues 311-319. I also have a structure of a homologue in which this loop is not missing, and I was hoping to use this as a template to model the missing loop. I've been using: http://www.salilab.org/modeller/wiki/Missing <http://www.salilab.org/modeller/wiki/Missing%20residues> residues as a guide. Briefly, I generate an initial model of the loop in 1M80 by filling in the sequence of the missing residues and aligning with the sequence in 1M80, inserting gaps for missing residues. This model is then used (with the inifile parameter under the automodel class), along with an alignment of the filled in 1M80 sequence with the homologous structure, to actually homology model the loop. As I don't want the rest of the protein to move, in both of these steps, I'm modifying select_atoms to include only the residues in the loop. The resulting model looks pretty good in terms of the conformation of the loop. What I notice, however, is that the geometry is a little bad where the loop reconnects with the rest of the protein. For example, the peptide bond between residues 310-311 and 319-320 is about 1.55 angstroms (ideal being ~1.33). I've tried "optimizing out" this issue with approaches like: a.library_schedule=autosched.slow a.max_var_iterations=500 a.md_level=refine.very_slow a.repeat_optimization=5 .and even increasing repeat_optimization to 25 cycles. This doesn't seem to help. Also, expanding the residues included in the optimization (from 311-319 to 310-320, for example) just moves the bad geometry to the boundary of that new window. Any ideas on what I'm doing wrong? Or how to fix the geometry within modeller? Thanks for the help! Omar Davulcu

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