March 2012 - modeller_usage

Error: Ran out of slaves to run tasks
by Xiao-Ping Zhang 16 May '12

16 May '12

Dear Modellers, When I was refining loops for a model in parallel, I asked modeller to generate 9999 models. But modeller stopped at 1245 with the following error. The computer has six cores, modeller uses four of them. The other two cores were free. Thank you for your help. <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1219> on <Slave on localhost> completed <Loop model building task #1.1217> on <Slave on localhost> completed <Loop model building task #1.1222> on <Slave on localhost> completed <Loop model building task #1.1218> on <Slave on localhost> completed <Loop model building task #1.1223> on <Slave on localhost> completed <Loop model building task #1.1224> on <Slave on localhost> completed <Loop model building task #1.1225> on <Slave on localhost> completed <Loop model building task #1.1226> on <Slave on localhost> completed <Loop model building task #1.1228> on <Slave on localhost> completed <Loop model building task #1.1229> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1227> on <Slave on localhost> completed <Loop model building task #1.1230> on <Slave on localhost> completed <Loop model building task #1.1232> on <Slave on localhost> completed <Loop model building task #1.1233> on <Slave on localhost> completed <Loop model building task #1.1234> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1235> on <Slave on localhost> completed <Loop model building task #1.1237> on <Slave on localhost> completed <Loop model building task #1.1238> on <Slave on localhost> completed <Loop model building task #1.1239> on <Slave on localhost> completed <Loop model building task #1.1240> on <Slave on localhost> completed <Loop model building task #1.1241> on <Slave on localhost> completed <Loop model building task #1.1242> on <Slave on localhost> completed <Loop model building task #1.1243> on <Slave on localhost> completed <Loop model building task #1.1244> on <Slave on localhost> completed <Loop model building task #1.1245> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> Traceback (most recent call last): File "refine_loop.py", line 41, in <module> a.make() File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 190, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 208, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/local/lib/python2.7/site-packages/modeller/parallel/job.py", line 136, in run_all_tasks raise ValueError("Ran out of slaves to run tasks") ValueError: Ran out of slaves to run tasks XP

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model quality: GA341, DOPE and zDOPE
by richard k belew 29 Mar '12

29 Mar '12

i'm trying to evaluate models generated by Modeller in comparison to some built using threading methods (ITasser). GA341 seems the primary coin-of-realm in Modeller-land, but depends on seqID and so this can't be used (i don't think?) on threaded models. DOPE can be, and normalized zDOPE seems recommended for comparison of models from different homologues. but in trying to compare models, i'm finding Modeller models that have excellent (> 0.8) GA341 scores but pretty terrible (1 - 1.5) zDOPE scores. and so in comparison to ITasser models with good zDOPE scores (~ -0.5), these threaded models would seem preferred? beyond the main CASP results, does anyone else have experience trying to compare threaded vs. homologue models in terms of these metrics, or others? thanks for any leads, rik

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DNA-protein complex modelling discrepancy!!
by Sumedha Roy 29 Mar '12

29 Mar '12

Hello I tried modelling a new complex based on a template complex with the same DNA ligand but a few mutations in the protein. Initially I did the modelling the usual way and got good detectable RMSD (about 0.6) with the new mutated PDB (just the new protein, didn't have the DNA) and the original complex. However when I tried to do the modelling considering DNA as a ligand (changed all DNA ATOMs to HETATM and modified alignment file with 9 appended '.'s - as my DNA is 9bp long), the new mutated complex, is nearly SAME as the template complex with minor changes in coordinates. (0.1 RMSD) I don't understand that if I am using the same template and mutations, why is there so much of a difference (nearly 0.5 RMSD) between the two new complexes (with and without the DNA). All RMSDs were done by superimposing structures in PyMOL. Please help, I'm terribly confused! Regards -- Sumedha Roy

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 35
by Ashish Runthala 29 Mar '12

29 Mar '12

Dear Sumedha, You are being confused with the assessment results, but they are correct. As you have stated, you modelled protein with, without DNA(using as a ligand) and got the RMSD difference between the models as 0.5A' in RMSd, when screened against the selected template. But this is obvious. The model with 0.1RMSD has probably better localized topology spanned over the 9bases of DNA. Check out the TM-Score of the two models against the template. As you have not provided further details about the protein length, the two models, and the template, it is difficult to precisely conclude something. TM-Score will answer your query the best. 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, March 28, 2012 4:02:12 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 35 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. mutate_selection.py (ARVIND PAL) 2. Re: mutate_selection.py (Modeller Caretaker) 3. Re: Regarding protein 3D structure modeling (Modeller Caretaker) 4. DNA-protein complex modelling discrepancy!! (Sumedha Roy) ---------------------------------------------------------------------- Message: 1 Date: Mon, 26 Mar 2012 12:49:18 +0530 From: ARVIND PAL <arvind.sbt(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] mutate_selection.py Message-ID: <CAMw18pPwUrHq13ZNb5Pu_fqe6ms4Nmg6z9cH7igxmM99w6E+TA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear sir when i am running the *mutate_selection.py<http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py> command i got the error selection contains no atom. what does it means. plz help me. *

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Model Clustering
by Ashish Runthala 28 Mar '12

28 Mar '12

Dear Modellers, I am facing some problem with the recently obtained results. Is there any way to improve the models through salign-iterative.py? The script calculates the percent topology of optimal superimposition. But, when implemented over a set of considered near-native decoys, it fails to further improve the topology (not even a bit of TM-Score undoubtedly and consistently) any single time. Rather, sometimes, the model accuracy was further decreased in terms of GDT-HA. However, this is expected as it would have taken the average overall model topology (as clear from the mutually slided model sequences in the alignment file when employed in model-multiple.py). Is there any way to precisely delimit the boundaries, where there is a huge difference (more than a specified threshold) in the backbone distance map, probably with salign-iterative so that the local model topology could be relaxed? Calpha distance 3.5A' is employed. Even with its alterations, expectations were not met. If this is incorrect, what is the mistake. Or, Is there any other way to cluster some good models through MODELLER? Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] Regarding protein 3D structure modeling
by Modeller Caretaker 26 Mar '12

26 Mar '12

On 3/26/12 1:30 AM, vishal Nemaysh wrote: > Regarding this (3D structure prediction) problem sir i will try to find > out some template for covering the whole query sequence during BLAST. > but there is no any single template or multiple template are found to > occupied this query. so sir plz suggest me some solution... Modeller is a package for comparative modeling, so if you have no template, you are out of luck. You either need to try harder to find a template (BLAST is not that sensitive - you can try other methods that use profile or HMM information, for example) or settle for only modeling the part of the sequence for which a template is available. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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mutate_selection.py
by ARVIND PAL 26 Mar '12

26 Mar '12

Dear sir when i am running the *mutate_selection.py<http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py> command i got the error selection contains no atom. what does it means. plz help me. *

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Regarding protein 3D structure modeling
by vishal Nemaysh 24 Mar '12

24 Mar '12

Hello Sir or all group members, i have an amino acid sequence and the length is (1106 amino acid). so plz tell me how can i model the complete 3D structure of this much lengthy sequence. thanking you, Your Sincerely -- Vishal Research Scholar, University of Delhi, North Campus Delhi-110007 M: 91+9650736653

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homology modelling with multiple subunits
by Zumot, Elia Nabil 22 Mar '12

22 Mar '12

Dear all, Is there a way to generate a homology model using several subunits as template? The protein I wish to model is a homotrimer. Am I wrong or is what is explained in "Building a model from multiple templates" not relevant here since I need the three subunits together in space (without steric clashes). Thank you in advance Elia Zomot Elia Zomot, PhD Computational and Systems Biology Department School of Medicine, University of Pittsburgh 3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213 Voice: 412 624 8699 - Fax: 412 648 3163 enz1(a)pitt.edu

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Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)?
by Valerio Lupperger 22 Mar '12

22 Mar '12

Hi, I use MODELLER (9.10) in a c-program like in http://salilab.org/modeller/manual/node456.html. As input I have one structure and its restraints. Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x,y,z)? And if so, how is it possible? Thanks, Valerio

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