February 2002 - modeller_usage

Using NAD
by bessiew 19 Feb '02

19 Feb '02

Dear Modeller, I'm using Modeller6v1 now. I'm so happy that in the library there is NAD and NADH so that I could get the homology with NAD or NADH in it not as heteratom. But I'm having problem in including NAD. In the file restyp.lib, the symbol for NAD or NADH is #. What symbol should I use to represent NAD or NADH in the alignment file, Using # or I should make some definition for them? Any kind help is highly appreciated. Sincerely, Mengmeng Wang

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** MODELLER SUPPORT ** RE: Hai modeller people!!!!!!!!
by Bozidar Jerkovic 19 Feb '02

19 Feb '02

Hi, Yes, that's a good idea. You can also try to use THREADER. For more resources and information please visit: http://salilab.org/bioinformatics_resources.shtml Can you please post all replies and questions directly on the list. Thanks, Bozidar On 20/2/02 1:06 PM, "skumar(a)www.cdfd.org.in" <skumar(a)www.cdfd.org.in> wrote: > > Dear Bozidar, > > Thank you very much for your reply. I have one idea kindly suggest me whether > it is worth of doing it?. > > The part of the target sequence which has insertions in the alignment when > compared to the template structure can we take out that region along with > some anchor residues and search it against fold recognition servers such > as FUGUE server and get the possible template structure against that region > and include that template in the ali file. > > Kindly suggest me your suggestions regarding this.Thank you very much in > advance. > > Yours sincerely, > Senthil kumar.R > > ---------REPLY TO------------- > Date:Tue Feb 19 18:07:14 GMT+00:00 2002 > FROM: Bozidar Jerkovic <bozidar(a)oboe.rockefeller.edu> > To: 'R Senthil Kumar' <skumar(a)www.cdfd.org.in>, > modeller_usage(a)salilab.org > CC: 'Bozidar Jerkovic' <bjerkovic(a)mail.wesleyan.edu> > Subject: ** MODELLER SUPPORT ** RE: Hai modeller people!!!!!!!! > > Hi, > > There is probably not much that you can do to get a model of 3D > structure for that sequence segment, although ab initio modeling with > some of the best methods has some chance of giving you a roughly correct > fold since this is a small domain of a larger protein, I presume. For ab > initio methods, check out the 2000 Progress review by David Baker in > Nature. > > What kinds of template search did you tried? Don't rely only of > MODELLER's SEQUENCE_SEARCH. Check out other methods at our web site: > http://salilab.org/bioinformatics_resources.shtml > > Thanks, > Bozidar > > > *********************************************** > -----Original Message----- > From: owner-modeller_usage(a)salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of R > Senthil Kumar > Sent: Tuesday, February 19, 2002 8:12 PM > To: modeller_usage(a)salilab.org > Subject: Hai modeller people!!!!!!!! > > > > Dear modellers, > > I am having a doubt in homology modelling.Please help me to overcome > this problem. > > I am having a template/target alignment file like this: > >> P1;xxx (template alignment) > -------------------------EPTIHKLAGCTA and go on. >> P1;xxx(taget sequence to be modelled) > MTGCATDAERAEPTIGCTAADEGRAEPTIHKLAGCTA and go on. > > My question is how to model the region in target sequence that doesn't > have any corresponding coordinates to get from template > sequence.(reference structure). > > Kindly suggust me solution to overcome to this problem.Thanks in > advance. > > Yours sincerely, > Senthil kumar.R > > R.Senthil Kumar, > Junior Research Fellow(JRF), > c/o Dr.Akash Ranjan, > Computational & Functional Genomics Group, > Centre For DNA Fingerprinting & Diagnostics (CDFD), > Hyderabad-500 076. > > Ph:040-7151344-Extn(Lab:1304) > (Hostel:2300) > E-mail:skumar@www.cdfd.org.in > > > > > > > > > > > > > > > > > > > > > > - > > >

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Hai modeller people!!!!!!!!
by R Senthil Kumar 19 Feb '02

19 Feb '02

Dear modellers, I am having a doubt in homology modelling.Please help me to overcome this problem. I am having a template/target alignment file like this: >P1;xxx (template alignment) -------------------------EPTIHKLAGCTA and go on. >P1;xxx(taget sequence to be modelled) MTGCATDAERAEPTIGCTAADEGRAEPTIHKLAGCTA and go on. My question is how to model the region in target sequence that doesn't have any corresponding coordinates to get from template sequence.(reference structure). Kindly suggust me solution to overcome to this problem.Thanks in advance. Yours sincerely, Senthil kumar.R R.Senthil Kumar, Junior Research Fellow(JRF), c/o Dr.Akash Ranjan, Computational & Functional Genomics Group, Centre For DNA Fingerprinting & Diagnostics (CDFD), Hyderabad-500 076. Ph:040-7151344-Extn(Lab:1304) (Hostel:2300) E-mail:skumar@www.cdfd.org.in

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objetive function in Modeller and z score in Prosa
by Violet Chang 18 Feb '02

18 Feb '02

Hi Modellers, I have a question regarding the objective function in the output file(.B99....) of MODELLER. I've been evaluating the models that run by MODELLER. I selected three best models from my running results based on their objective function( the lower the better). Each objective function of them is like following: A: 6103.3325, B: 6090.5195, C: 6077.6436. Then I used ProsaII to calulate the z- scores after I did CHARRM energy minimization. The zp-comb of them are A: -5.69, B: -3.82, C: -5.87. >From Modeller I can see B and C might have better models than A does. But from ProsaII, I can exclude B. Does this kind of thing happen before? I'd like to know if I should include as many as models I have to run Prosa, in case the models with higher objective functions have lower z-scores. Thank you very much. Sincerely, Violet

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TRANFER_XYZ (cluster_cut>0)
by Obdulia Rabal 18 Feb '02

18 Feb '02

Hello. Thank you for your answer about the modelling loops ( date: 14/02) Now, I have a problem with the different commands. I have the main template I want to use to build the model and several small templates I only want to use to model the loops. My alignment looks like: Main template: -------Leu-His-Gly-Tyr-Phe-Val-Phe-Gly-Pro-Thr-Gly-------------- Loop's templates:------___-Ala-Asn-Trp-Tyr-___-Phe------------------- Loop's templates:---------------------------- Phe-Gly-Asn-Phe-Leu Loop's templates::-------------Asn-Trp-Phe-___-Phe-Gly-Asn Target:--------------Val-Ala-Asn-Trp-Tyr-___-Phe-Gly-Asn-Phe-Leu and I want to run the following commands: MALIGN3D TRANSFER XYZ ( with a CLUSTER_CUT >0) My problems are: 1º) As I have understood, the command MALIGN3D doesn't work because there aren`t equivalent positions during the framework construction betweeen the first template and the rest. Am I wrong? So I try to solve this by superposing the loop's templates with the main template with the command SUPERPOSE. 2º) After, when I run TRANFER XYZ ( CLUSTER_CUT >0), it appears in the .log : transfe_505_> MODEL is an average of the largest cluster: 1.0000 transfe_336E> No template structures. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I don't know what's my error. Do I need more templates to make a cluster? Must the loop's templates be similar to the first template in order to have the same topology? Don't they overlap properly? Is TRANFER XYZ ( CLUSTER_CUT =-1.0) the only possibility I have? (because it works) Thanks in advance

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** MODELLER Support ** TEST PLEASE IGNORE
by Bozidar Jerkovic 18 Feb '02

18 Feb '02

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mkspline_E
by Luca Settimo 18 Feb '02

18 Feb '02

Dear modeller, I was using still modeller 4 (just to complete one work that I was doing) I have one problem, I m building a model using 7 templates (I made a structural alignment that I am using to build my model). Everything works fine... except that for one situation (so my input file top and ali are correspondent, except the sequence that I have to model... like you can immagine) and I have this message: mkspline_E> too many parameters, increase MPRMCNS if I remove one template it works fine... what does it mean this message? how can I still use 7 templates? Luca ................................................................... Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo

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bug report
by vuissoz Jean-Marc 16 Feb '02

16 Feb '02

dear modeller team, Probably something is not installed correctly on my version of modeller6.1 but I don't find what, here are the log files en top files with the error reported. best tanks vuissoz jean-marc >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: >2.00:-1.00 AYVINDSCIACGECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED* SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'prot.ali' SEQUENCE_SEARCH ALIGN_CODES = '1fdx', DATA_FILE = ON MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 IRIS 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/15 17:44:24.629 read_se_367E> Sequence not found; code: P1;1xnb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2306323 2252.269 2.199 Starting time : 2002/02/15 17:44:24.629 Closing time : 2002/02/15 17:44:33.146 Total CPU time [seconds] : 0.00

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strand restraints
by Reuter Nathalie 15 Feb '02

15 Feb '02

Dear modellers, we use Modeller6 and we have some problems restraining beta-sheets in our model. The student working on this project sent an -email to the forum a few days ago and since then we have tried many different things to try to analyze the problem so we send more precise questions. We tried to restrain beta strands in our model, using the RESTRAINT_TYPE = 'SHEET' or RESTRAINT_TYPE = 'STRAND' . All our tests were unsuccessful. Last thing we tried was to force beta strands in the model to be longer than they are without special restraints. That means, in the previous model, there are beta strands (they exist in the template structure) without adding other special restraints in the top script. I thus think it should be possible to make them slightly longer. But if I try to apply special restraints to increase their length, the strands completely disappear in the models. The .top file is OK, modeller can read it, there are no error messages in the .log file, the .rsr file contains additionnal restraints (dihedral pairs) with regards to the same calculation without any restraint. The .V files are also different with or without the special restraints. So everything seems to be OK, but the models never contain these additionnal beta strands. The longer the strands we try to restrain, the more violations (in the log file) there are but their magnitude is not significantly higher than when I apply an 'alpha' restraint (which works perfectly well, i.e. it appears in the model whatever the region we try to introduce it in). To force strand (or even beta-sheets) never worked. So it looks like restraining strands and beta-sheets is much more difficult than alpha-helices, which we can introduce almost anywhere in the model. Here are our questions : Is it normal to be able to force an alpa helix wherever you want and not a beta, and if yes why ? Are the violations due to beta strands too penalizing ? Shall we modify the optimization schedule and if yes, which parameters should we change ? Is it possible to exclude block of atoms from the optimization procedure of the objective function ? Thanks, Nathalie Reuter -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65 -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65

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How to model DNA binding protein
by Michael Buck 14 Feb '02

14 Feb '02

How can I include the DNA structure when modelling a DNA binding protein? Can I just include the HETATM atoms using SET MODEL_TOPOLOGY = 1, HETATM_IO = on This doesn't seem to work, what else to need to include? Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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