March 2012 - modeller_usage

Re: [modeller_usage] 2. loop refinement (rjayashree13-science@yahoo.co.in) from modeller_usage Digest, Vol 11, Issue 32
by Jan H. Löhr 22 Mar '12

22 Mar '12

>Message: 2 >Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) >From: rjayashree13-science(a)yahoo.co.in >To: modeller_usage(a)salilab.org >Subject: [modeller_usage] loop refinement >Message-ID: > <1332393995.15170.YahooMailClassic(a)web193505.mail.sg3.yahoo.com> >Content-Type: text/plain; charset="utf-8" > >There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. > >How can one decide which residues need refinement? > > >Dr. Jayashree Ramana You will find a nice example in the modeller tutorial. Hoping you may better grasp the general idea, I am attempting to rephrase the gist: The residues that need to be refined usually have a high energy. Probably because your alignment was not optimal in this position, or because you do not have any information from the template(s) because of missing residues in the templates PDB or because of an insertion in the target sequence. So when you align your template and your modeller structure in a molecular imaging program you will probably see that some residues in your model do not have a corresponding template residue (naturally, this is obvious from sequence alignment as well). When there is no information from the template, modeller cannot do comparative modeling and therefore these residues will probably not be modeled well. These residues (along with residues that have been poorly modeled for other reasons) are easily spotted by the assessment-methods within modeller. I recommend looking at an energy profile such as the DOPE profile. Comparing the graphs of template and model, you will see residues that need optimization (residues whose DOPE-pseudoenergy is much higher for the model than for the template). Be careful though because of different residue lengths of template and target the DOPE profiles are not always strictly superimposable for corresponding residues may not have the same number (again because of insertions, missing residues, etc.). Summing up: You may already know the residues. Look at the alignment and identify regions where the template provides no information for your target. Try to identify these and possibly other problematic regions by using the assessment methods and obtain the DOPE profile. Actually, the answers you seek are in the end of tutorial 1 ("Basic Modeling") and at the beginning of tutorial 2 ("Advanced Modeling) along with code examples to assess your model at http://salilab.org/modeller/tutorial/. That should do the trick. Cheers Jan Jan H. Löhr Univ. Hamburg, Germany -----Original Message----- From: modeller_usage-bounces(a)salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of modeller_usage-request(a)salilab.org Sent: Thursday, March 22, 2012 3:55 PM To: modeller_usage(a)salilab.org Subject: modeller_usage Digest, Vol 11, Issue 32 ------------------------------ Message: 2 Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) From: rjayashree13-science(a)yahoo.co.in To: modeller_usage(a)salilab.org Subject: [modeller_usage] loop refinement Message-ID: <1332393995.15170.YahooMailClassic(a)web193505.mail.sg3.yahoo.com> Content-Type: text/plain; charset="utf-8" There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. How can one decide which residues need refinement? Dr. Jayashree Ramana

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calculate energy for a 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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loop refinement
by rjayashree13-science＠yahoo.co.in 21 Mar '12

21 Mar '12

There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. How can one decide which residues need refinement? Dr. Jayashree Ramana

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ALIGN_CODES(i) error, Again
by Zumot, Elia Nabil 19 Mar '12

19 Mar '12

Hello Modeller people, I realize this error has been posted repeatedly and I have tried to check for all possible solutions mentioned but I still can't do it right. My alignment filename is 2nwx_ASCT.ali and my pdb filename is 2nwx_A.pdb so the names and letter cases match exactly. The error I'm getting is: ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ASCT The script and alignment files are below. Thank you in advance for the help Elia Zumot The script I use with modeller version 9.10 on Linux is: from modeller import * from modeller.automodel import * env = environ() def do_align(): a = automodel(env, alnfile='2nwx_ASCT.ali', knowns='2nwx_A', sequence='ASCT', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() do_align() and my alignment file (2nwx_ASCT.ali) is: >P1;2nwx_A structure:2nwx_A.pdb:4:A:416:A:::: EYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPAR- LGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGG---------QQFQPHQAPPLVHILLDIV PTNPFGALANG----------------------------------------------------QVLPTIF FAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQG--VHV VGELAKVTAAVYVGLTLQILLVYFVLLKIY-GIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKE-M GISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIM LAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE* >P2;ASCT sequence:ASCT:4::::::: RNAFVLLTVTAVIVGTILGFTLRPYRMSYREVKYFSFPGELLMRMLQMLVLPLIISSLVTGMAAL-DSKA SGKMGMRAVVYYMTTTIIAVVIGIIIVIIIHPGKGTKENMH-------REGKIVRVTAADAFLDLIRNMF PPNLVEASFKQFKTNYEKRSFKVPIQANETLVGAVINNVSEAMETLTRITEELVPVPGSVNGVNALGLVV FSMAFGFVIGNMK--------EQGQALREFFDSLNEAIMRLVAVIMWYAPVGILFLIAGKIVEMEDMGVI GGQLAMYTVTVIVGLLIHAVIVLPLLYFLVTRKNPWVFIGGLLQALITALGTSSSSATLPITFKGLEENN GVDKRVTRFVLPVGATINMDGTALYEALAAIFIAQVNNFELNFGQIITISITATAASIGAAGIPQAGLVT MVIVLTSVGLPTDD------ITLIIAVDWFLDRLRTTTNVLGDSLGAGILHHLN* 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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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 30
by Alexander Predeus 16 Mar '12

16 Mar '12

Dear Ashish, thank you for your suggestions! I have some follow-up questions though. 1. Did you mean some simplified replica exchange with MODELLER or a real replica-exchange simulation? Because simple temperature replica exchange is most probably not feasible for a system of this size - number of replicas necessary to achieve the same exchange rates grows as ~ sqrt (N) and will be too high in this case. 2. As for increased temperature MD for loops - you imply that I keep the structure restrained and only let loops relax? I was under the impression MODELLER's refinement does something of this sort in CG model, which should be a lot faster than AA MD anyway. 3. About the normalized DOPE - again, I was under the impression that it only matters when you are comparing different proteins. My task is only to compare different models of the same protein. Thank you in advance! -- Alex Predeus, MSU

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Re: [modeller_usage] Loop Modeling in a Protein-DNA Complex
by Modeller Caretaker 16 Mar '12

16 Mar '12

On 3/16/12 12:36 PM, Alexander Predeus wrote: > Thank you very much for your prompt response! > > I have a small follow-up question. I was under the impression that > refinement is essentially and MD simulation, and thus if I start two > scripts, requesting to generate a 100 models in each, I would end up > with 200 different models. > > I was surprised to see that the scripts actually generate precisely the > same series of models, and with same energies etc. > > Why is that? Is there a way to run several parallel simulations and get > independent sampling, or does it have to go consecutively? Modeller results are reproducible, so yes, given the same input conditions (including scripts, Modeller version, and operating system) you'll get the same outputs. If you want to get different results, set a different random seed for each of your runs using the rand_seed argument to environ(): http://salilab.org/modeller/9.10/manual/node111.html 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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Re: [modeller_usage] Loop Modeling in a Protein-DNA Complex
by Alexander Predeus 16 Mar '12

16 Mar '12

Thank you very much for your prompt response! I have a small follow-up question. I was under the impression that refinement is essentially and MD simulation, and thus if I start two scripts, requesting to generate a 100 models in each, I would end up with 200 different models. I was surprised to see that the scripts actually generate precisely the same series of models, and with same energies etc. Why is that? Is there a way to run several parallel simulations and get independent sampling, or does it have to go consecutively? Thank you again! -- Alex Predeus MSU

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Loop Modeling in a Protein-DNA Complex
by Alexander Predeus 15 Mar '12

15 Mar '12

Hello all, I'm trying to fill the gaps in a protein-DNA complex of a moderate size (~ 15k heavy atoms). There are two protein chains with 13 missing pieces overall, most are 2 to 8 AA, but two are fairly long (~ 15 AA). I'm modeling ONLY the missing parts for I don't want the X-ray structure perturbed, and I included DNA molecule as a ligand (with HETATM identifier and "." in alignment). >From reading this mailing list, I've realized that it's better to generate a lot of models using a faster routine (e.g. refine.very_fast) and then take the best one, rather than do longer refinement and generate less models. The question I wanted to ask, is what is the best assess method I can use, considering the nature of my task? I'm using DOPE right now, but in the manual I've also seen mentioning of DOPE-HR. Would it slow down the loop refinement process a lot (or at all)? Thank you for any suggestions. -- Alex Predeus Michigan State University

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Regarding .tree
by Ashish Runthala 12 Mar '12

12 Mar '12

Dear Modellers, How is the evolutionary tree .tree file constructed for multiple templates through salign_multiple_struc. What algorithm is used? Is it ML, MP, NJ, or anything else. Regards, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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(no subject)
by pawan raghav 11 Mar '12

11 Mar '12

http://demos.mclanka.com/aquanew/BIT/admin/BIT-debug-backup/BIT-debug/PEAR/…

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