- modeller_usage - salilab.org

Re: Modeller input alignment file
by Modeller Care 16 Jun '03

16 Jun '03

forwarded for majordomo reasons ---------------------------------------------------- Hello Christos, you will find the information you seek at http://salilab.org/modeller/manual/node83.html#alignmentformat , and an example from the user-list: http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modelle r_usage.archive.02/Author/article-437.html For short, 2:@:386:@ means: number_first_aminoacid_in_pdb_file:name_of_chain:last_aminoacid:name_of_ chain, so if your structure has the first 10 aminoacids missing, the last aminoacid available is numbered 432, and the chain is named "B" in the pdb-file, then this should be 11:B:432:B . Best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz ------ End of Forwarded Message

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FW: Modeller6v2 trouble
by Modeller Care 12 Jun '03

12 Jun '03

------ Forwarded Message From: Mario Garcia <sbioi000(a)cib.csic.es> Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) To: modeller-care(a)salilab.org Subject: Modeller6v2 trouble Dear Dr. Bozidar, I have some error after a modeling jot execution (mod script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding .top and .ali input files and the resulting .log file. Could you give some hints to help me? Thank you very much in advance for your help. Regards, Mario Garcia. ------------------------------------------------------------------------- Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario(a)cib.csic.es C.S.I.C. c/ Velazquez, 144 28006-Madrid. SPAIN. ------------------------------------------------------------------------- ======================MOB3.top=================================== # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'MOB4.ali' # alignment filename SET KNOWNS = '1cii' # codes of the templates SET SEQUENCE = '1mob' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling ================MOB4.ali================================ C; mob_1cii.phy align >P1;1cii structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN KFW* >P1;1mob sequence:1mob ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE -------------------------------RGKLNSEAKHKTVAEFKRA MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- ---* =====================MOB4.log================================= MODELLER 6v2, 17 Feb 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 akilonia 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' TOP_________> 106 706 SET KNOWNS = '1cii' TOP_________> 107 707 SET SEQUENCE = '1mob' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/03/21 23:47:53.033 Closing time : 2003/03/21 23:48:02.202 Total CPU time [seconds] : 0.00 ------ End of Forwarded Message

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RE: problem in installing modeller
by Andrej Sali 11 Jun '03

11 Jun '03

Hopefully somebody on modeller_usage(a)salilab.org will respond. a -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: hjslfad lhasfh [mailto:pannirselvam_m@yahoo.com] > Sent: Tuesday, June 10, 2003 7:15 AM > To: sali(a)salilab.org > Subject: problem in installing modeller > > > respected sir/madam, > > while installing the modeller, i > encountered a peculiar problem. The installation of > files was proper, but when i try to run 'mod6v2' > executable file in modeller's bin directory, i am > getting the error message as "command not found". > > so kindly provide me with further > information to install the program > > yours sincerely > > pannir > > __________________________________ > Do you Yahoo!? > Yahoo! Calendar - Free online calendar with sync to > Outlook(TM). http://calendar.yahoo.com >

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MULTIPLE/SINGLE templates for modelling.
by Mr.Sridhar 10 Jun '03

10 Jun '03

I have two basic questions which I am desperate to get answers. Any body there who can help me ? ----------------------------------------------------------------------- 1. In homology based modelling is it good to use single template or multiple templates? I have a cytochromep450 protein which shares maximum homology with another protein of same class . But there were some missing residues in the template. When used for modelling the region corresponding to this missing region had bad environments in Verigy3D. I went on for loop modelling for this region. But is this a good approach ? I feel the alignment itself should take care of everything. I heard about using multiple templates in such cases. How is this approach followed and how good is it ? -------------------------------------------------------------------------- 2. I need to model some point mutations into this same protein sequence. What is the best way of introducing mutations. Should the mutations be introduced in the sequence and then modelled seperately, or should they be introduced in the model of the wildtype ? I want to do molecular dynamic simulations on Wildtype and Mutants to compare and contrast the wildtype and mutant structures. What effect would both these approaches have on the correctness of my results. ---------------------------------------------------------------------------- I'll be very grateful to you for your patience for all your suggessions for my quieries. Thanking you, sridhar

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Re: FW: model a protein
by Eric Feyfant 02 Jun '03

02 Jun '03

You should check the Align2D command Eric ------------------------------------ Eric Feyfant, Ph.D. Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant(a)wyeth.com >>> Modeller Care <modeller-care(a)salilab.org> 06/02/03 12:18PM >>> Forwarded by the list owner ----------------------------------------------------- Dear Sir, I have a few questions before starting modelling. I would like to know how one can use modeller for aligning the sequences that have the structure (treated as templates for modelling) and that do not have a solved structure (our target). I couldn't get the answer for this question from the modeller tutorial. Expecting the answer as soon as possible. Thanking You Nethaji

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FW: model a protein
by Modeller Care 02 Jun '03

02 Jun '03

Forwarded by the list owner ----------------------------------------------------- Dear Sir, I have a few questions before starting modelling. I would like to know how one can use modeller for aligning the sequences that have the structure (treated as templates for modelling) and that do not have a solved structure (our target). I couldn't get the answer for this question from the modeller tutorial. Expecting the answer as soon as possible. Thanking You Nethaji

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Command for distance restraint
by Modeller Care 28 May '03

28 May '03

non member submission forwarded by list owner --------------------------------------------------------------- Hi, Iam new to modeller. Can anyone tell me what is the command for restraining the distance between two specified atoms. thank you, sujatha ------ End of Forwarded Message

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Problem with _ and - characters present in filenames
by Owen 27 May '03

27 May '03

I have recently started using modeller 6v4 (previously using modeller 4). When I ran identical files on 6v4 I got the error seen in the log file below. An example of the type of filename for .top and .ali files is this: P42460_3-TPR-317-350.ali When I removed all the _ and - characters from the filenames, and from the relevant lines in the top and alignments, the model was built no problems. Is there a reason why these characters are no longer allowed in modeller 6v4 and if so, is there a way to make it recognise them to save alot of time having to rename all my files? Thanks! MODELLER 6v2, 17 Feb 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 wolf 6.5 IP27 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/05/27 14:13:21.725 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2003/05/27 14:13:21.725 Closing time : 2003/05/27 14:13:26.674 Total CPU time [seconds] : 0.00

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FW: MALIGN-3D: How to run it.
by Modeller Care 22 May '03

22 May '03

Message forwarded by list-owner ------ Forwarded Message From: "Mr.Sridhar" <sridhar(a)www.cdfd.org.in> Date: Thu, 22 May 2003 10:45:33 -0700 To: Modeller Care <modeller-care(a)salilab.org> Subject: MALIGN-3D: How to run it. Sir, I'll be very much grateful to you if you can help me in one of my modeller job submission. I am trying to superimpose some structures simultaneously using malign3D. My top script file and alignment file are as follows. I had attached the log file also. There structures were of ~410 residues and with heme and a bound ligand. I always failed to get the structural alignment, the reason I could not figure out. Please help me in running this program, also tell me what are the general steps to follow for doing structural alignments and where are the chances for potential errors. ###########################TOP SCRIPT################## SET OUTPUT_CONTROL = 1 1 1 1 2 SET STOP_ON_ERROR = 1 SET MAXRES = 2000 READ_ALIGNMENT FILE = 'str.ali' SEQUENCE_TO_ALI SET ALIGN_CODES = '1dz8' '2cpp' SET ATOM_FILES = ALIGN_CODES SET ATOM_FILES_DIRECTORY = './' MALIGN3D SET ADD_SEQUENCE = on SET CURRENT_DIRECTORY = on SET OUTPUT = 'LONG' SET GAP_PENALTIES_3D = 0.0 1.75 SET FIT_ATOMS = 'CA' SET WRITE_FIT = on SET WRITE_WHOLE_PDB = on WRITE_ALIGNMENT FILE = 'str_STR.pir' SET ALIGNMENT_FORMAT = 'PIR' #######################ALIGNMENT FILE###################### >P1;1dz8 structureX:1dz8: 11 :A: 414 :A:undefined:undefined: 9.99: 9.99 -----LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIQRPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* >P1;2cpp structureX:2cpp: 10 : : 414 : :undefined:undefined: 1.63: 9.99 ----NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPER IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV* ########################################################## Thanking you sridhar ------ End of Forwarded Message

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Re: RMSDs including experimental error
by Modeller Care 21 May '03

21 May '03

Non-member submission forwarded by the list owner ---------------------------------------------------------------------- Hi, This is a reply to "modeling question" by Douglas Kojetin, but may be useful for others interested in the difference between models and crystal structures: One way you can check for similarity to the experimental structure whilst including experimental error in a rigorous way is to calculate the RMSD weighted by the B-factors. I have a description of a method to do this in a paper in Proteins that is due to be online/published in a couple of days. Ref: Forrest LR, Woolf TB, "Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions", 2003. Essentially the method is this: define the 'experimental uncertainty' as a sphere around the atom coordinate, whose radius is dependent on the B-factor of that atom. This depends on the relationship between root mean square fluctuation and B-factor (B = 8 * pi^2 * RMSF^2 / 3). If the distance between the model atom and the xray atom (centers) is more than the radius of the sphere, then you define the effective distance as zero (the atom is within the 'experimental uncertainty'). If the model atom falls outside the sphere, then you subtract the radius of the sphere from the distance between the atom centers. Then you calculate the Root-mean-squared deviations of these effective distances, rather than the distances between the centers. I bet you find that the model of the 100% identical structure has a B-factor-weighted RMSD of less than 0.1A. Good luck, Lucy Forrest -------------------------------------------------------- Hi, for question 1, i think it is normal and expected that a model, even if built on a sequentially 100% identical template, will be somewhat different compared to an experimental solution. Although it should not go beyond let us say 0.5, or certainly not beyond 1.0 Ang RMSD. It is below the "experimental error" i.e. if the same protein is solved experimentally in different crystal forms, or at different resolution levels, or solved at high resolution but once by X-ray and once by NMR, you will still see an approx <1 Ang RMSD difference among the structures. So there is nothing special to see that your model is not exactly identical to the experimental one. for a reference you can look up figure 6 (and text) in chapter 7 (pp.167-206), book: Protein Structure (determination, analysis and applications for drug discovery) editor: DI Chasman, 2003 Marcel Dekker. question 2: it is a very interesting and useful survey that you did. Unfortunately it is difficult to generalize, because in each modeling case the set of available templates (their sequence identity to the target and structural variability with each other) is different. However your experiment about a proper "essay" is near exhaustive within your specific experiment, so you are certainly in a position to make a point. Of course the best would be to use instead of Procheck or other programs the actual experimental structures to verify the best "essay", e.g. re-model your protein A without the 100 % identical template and explore the same question you did for protein B. In this case you can compare your resulting models with the actual X-ray structure. Andras On Mon, 2003-05-12 at 15:52, Douglas Kojetin wrote: > please see the message, originally directed towards dr. sali, below. > > if anyone has any comments, please send them! > > many thanks, > doug kojetin > > Begin forwarded message: > > > Dr. Sali: > > > > I am a graduate student in the Department of Molecular and Structural > > Biochemistry at North Carolina State University. I have a question > > more about modeling process itself rather than the program MODELLER. > > > > I have used your program, MODELLER, to create models of a subfamily of > > proteins our lab and collaborators are interested in (total ~ 30). > > There are approximately 10 solved structures to the domain of > > interest. One of these solved structures (structure A) is in the same > > subfamily within the same species of proteins we are modeling (model > > A), whereas the other 29 proteins are of unknown solved structure. My > > question concerning the use of templates in the modeling process. > > > > ############## > > my main question > > ############## > > > > (if this is confusing, please let me know and i will rephrase) ... > > > > Would using a solved structure (structure A) to model a protein of > > exact sequence (model A) which will be used in a comparison of 29 > > other structures with no known structures (and lower 'homology' > > compared to that of structure A to model A -- which is 100%) bias > > model A? Overall, we are interested in comparing all 30 structures. > > This comes mostly from outside comments that our modeled protein does > > not look 'exactly' like the solved structure. As one would like it to > > look as close as possible to the solved structure, it is a model after > > all, and perhaps we just need to be more descriptive in explaining our > > results, especially pertaining to this specific model. > > > > ##################### > > how i modeled the proteins > > ##################### > > > > I performed a 'modeling parameter assay' to find the number of > > templates to use to model a protein (model B), ranging from 1 to ~8 > > templates. In addition, I 'assayed' the amount of refinement to use. > > > > Overall, I had an assay 'shaped' like a matrix with, for example, > > refinement across the top and # of templates going down. I produced 50 > > models for each and ran a variety of analyses on the models (including > > Ca RMSD to the most homologous protein, ERRAT, PROCHECK, etc) and > > computed the average 'value' output from the respective analyses. > > > > All in all, using four (4) templates and a refinement value of 1 > > produced the 'stereochemically best' models. > > > > I applied the same rationale to another protein of interest (model C), > > and the same trends were extrapolated. > > > > question > > --> is this rationale 'acceptable'? or how would you do something > > similar? > > > > Many thanks for your input, and I'm sorry for the long-winded email. > > > > Douglas Kojetin ------ End of Forwarded Message

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