- modeller_usage - salilab.org

In what are the initial structures different?
by BIN ZHANG 09 Apr '12

09 Apr '12

Dear All: I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual. For example, by using a = automodel() a.starting_model = 1 a.ending_model = 50 I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed. Thanks very much for help. Best, Bin

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Error in ALIGN_CODES(i)
by Sumedha Roy 09 Apr '12

09 Apr '12

Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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problem with Chain.join()
by Jan Kosinski 06 Apr '12

06 Apr '12

I cannot get Chain.join() working properly for multi-chain PDB files. For example, for PDB code 2YFH, which has chains A, B, C, D, E, F,: * when I join D and E I get A, B, C, D, F as expected * but if I try to join A and B I get A, F only To reproduce run the following script: ----- from modeller import * env = environ() mdl = model(env) mdl.read(file='2yfh') print "before:" for c in mdl.chains: print c mdl.chains['A'].join(mdl.chains['B']) print "after:" for c in mdl.chains: print c mdl.write('out.pdb') print "reading new file:" mdl1 = model(env) mdl1.read('out.pdb') for c in mdl1.chains: print c ------------ will print in the log: before: <Chain 'A'> <Chain 'B'> <Chain 'C'> <Chain 'D'> <Chain 'E'> <Chain 'F'> after: <Chain 'A'> <Chain 'F'> <Chain 'F'> <Chain 'F'> <Chain 'F'> reading new file: relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. relabel_469W> At least one residue number in the model is duplicated. (First duplication is residue " 1", chain " A".) Suggest you renumber the residues and/or chains to avoid selecting the wrong residues (e.g. with model_segment). <Chain 'A'> <Chain 'A'> <Chain 'F'> Tested with Modeller 9v8 and Modeller 9v9. Is it a bug or expected behavior? Best regards, Jan Kosinski

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problem in modeling protein with ligand
by NUTAN CHAUHAN 05 Apr '12

05 Apr '12

Hello all, I want to model my protein using template with its ligand bound to it. How can do this..i dnt hv idea. plz help. thnx in advance, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Saturday, 24 March 2012 10:27 PM Subject: modeller_usage Digest, Vol 11, Issue 34 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: 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)? (Modeller Caretaker) 2. Re: homology modelling with multiple subunits (Modeller Caretaker) 3. Regarding protein 3D structure modeling (vishal Nemaysh) 4. Re: Regarding protein 3D structure modeling (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Mar 2012 13:44:59 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Valerio Lupperger <valerio.lupperger(a)gmx.net> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] 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)? Message-ID: <4F6B8F4B.6020705(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/22/12 8:08 AM, Valerio Lupperger wrote: > 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? If you can do it in a Python script, you can generally do it with the C API (most of the Python interface to Modeller is simply calling the C API underneath, in the _modeller module). So you can write the equivalent Python code, and then look at Modeller's Python interface to see what the equivalent C API functions are that it's calling. For example, to calculate the energy you would call the energy() method in the selection class; if you look at modlib/modeller/selection.py you'll see that that method calls the C API mod_energy() function. In C you will have to manually keep track of memory and handle errors, of course, which is done automatically for you by the Python interface. 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: Thu, 22 Mar 2012 13:48:48 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: "Zumot, Elia Nabil" <enz1(a)pitt.edu> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] homology modelling with multiple subunits Message-ID: <4F6B9030.60402(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/22/12 10:53 AM, Zumot, Elia Nabil wrote: > 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). Unless I don't understand your question, this is covered by http://salilab.org/modeller/9.10/manual/node28.html Modeller is not going to magically determine the interface region between your subunits and dock them, of course. You need to give it information about the interface between subunits (either by giving it a multimeric template, or by supplying it with subunit-subunit restraints if you only have monomeric templates). 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: 3 Date: Sat, 24 Mar 2012 11:27:49 +0530 From: vishal Nemaysh <vishal.bioinfotech(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] Regarding protein 3D structure modeling Message-ID: <CALCM-RALrVh0c_NhOOVBKU_XvMQiFnnkyi-=18+1qHgasQWrJQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" 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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rmsd from template
by Matthias Schmidt 02 Apr '12

02 Apr '12

Hi, Is there a way to have Modeller calculate the RMSD from the template for each generated model? Best, Matthias

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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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