September 2005 - modeller_usage

difficulty in modelllllling a chimeric protein, plz help
by rathankar rao 09 Sep '05

09 Sep '05

hi all i have a difficulty in modelling a chimeric protein i dont know what is wrong in my ali file or in the top files. plz help. i have enclosed both of my files in it --------------------------------- Click here to donate to the Hurricane Katrina relief effort. # A sample TOP file for fully automated comparative modeling INCLUDE # include MODELLER routines SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files SET ALNFILE = 'alignment.ali' # input file w/ templates and target SET KNOWNS = '2PIA' '1GVH' '1TVC' '1KRH' '2CND' '1QGA' '1H42' '1FNC' '1RFK' # templates' PDB codes SET SEQUENCE = 'reduct' # target code SET STARTING_MODEL = 1 SET ENDING_MODEL = 3 SET HETATM_IO = ON SET OUTPUT_CONTROL = 1 1 1 1 1 CALL ROUTINE = 'model' # get alignment and a model >P1;2PIA StructureX:2PIA :8: :320: :Oxido:HUM: : FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW------------- ------------------------------------------------------------- ------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD* >P1;1GVH StructureX:1GVH :212: A :261:A :oxido:uk2: : ------------------------------------------------------------P D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TVC StructureX:1TVC :44:A:248:A :oxidored:uk3: : ---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL----------------------- ------------------------------------------------------------- ----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF FEKF---LPSG-------------------------------------------------- ------------------------------------------------------* >P1;1KRH StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------* >P1;2CND StructureX:2CND :145: :257: :oxidored:uk5: : ------------------------------------------------------------- -----------------------------------------------------------GS GITPMYQIIQAVLRDQPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQV KRPEEGWKYSVGFV-TEAVLREHVPEGGDDTLALACGPPPMIQFAISPNLE---------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1QGA StructureX:1QGA :194:B :231:B :oxidored:uk6: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE Q------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------* >P1;1H42 StructureX:1H42 :190:A :235:A :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE QKNPQ--GGR--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1FNC StructureX:1FNC :234: :281: :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------SRE QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI--------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1RFK StructureX:1RFK :4: B :91:B :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET* >P1;reduct Sequence:reduct:1 : :344 : :hypo:unknown: : FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD*

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Re: modeller_usage Digest, Vol 4, Issue 75
by rathankar rao 08 Sep '05

08 Sep '05

hi all i am facing a problem in modelling a chimeric protein. i need only certain regions of the protein to be modelled by one template and not the rest of them . so dont know what is wrong with my code, plz help me. i have enclosed the .ali , .top and .log files with regards rathankar modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit http://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: Internal error: array too small (Modeller Caretaker) 2. Tutorial for beginners? (Antonio Arroyo Luque) 3. Re: Tutorial for beginners? (Modeller Caretaker) 4. Re: Tutorial for beginners? (Karsten Suhre) ---------------------------------------------------------------------- Message: 1 Date: Thu, 01 Sep 2005 16:58:09 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] Internal error: array too small To: hchoe Cc: Modeller Message-ID: <43179591.2000607(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed hchoe wrote: > I've got this error message. > > dihdisn_223E> Internal error: array too small: > current maximum, current need: 100 101 > > What should be fixed? Thanks in advance.. Modeller has an internal limit of 100 on the number of Cys residues (which it uses while building disulfide bridge tables), which you have exceeded due to the large size of your system (do you really intend to model 31000 residues?). I don't think I'll be able to reproduce your problem here, because your input sequence doesn't appear to correspond to 1lp1 in the PDB. There is unfortunately no way that this limit can be circumvented, short of modeling a smaller protein, or waiting for us to release a new version of Modeller without this limit. 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: Mon, 05 Sep 2005 13:57:44 +0200 From: Antonio Arroyo Luque Subject: [modeller_usage] Tutorial for beginners? To: Modeller Message-ID: <431C32B8.3070003(a)upo.es> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello everyone, I try to lunch and run Modeller8v1 without any success. I use either the Windows or the Mac version of the program. The problem I have is that I don't know anything about Informatics but I want to learn. The tutorial of Modeller I've found assumes certain knowledge of Informatics. For instance, how do I launch Modeller? From the prompt of a OS terminal? How to say to the program where my files are located? I have this problem since version 6 of Modeller (more than 2 years ago) and since that I've been downloading new versions of the program but as I said without any success. Is there any basic, basic, basic (something like Modeller for Dummys - as I am) tutorial to start with? I will very appreciate your help. Also, any Spanish people working with Modeller? Thank you very much Antonio ------------------------------ Message: 3 Date: Mon, 05 Sep 2005 10:12:16 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] Tutorial for beginners? To: Antonio Arroyo Luque Cc: Modeller Message-ID: <431C7C70.9060800(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Antonio Arroyo Luque wrote: > I try to lunch and run Modeller8v1 without any success. I use either > the Windows or the Mac version of the program. The problem I have is > that I don't know anything about Informatics but I want to learn. The > tutorial of Modeller I've found assumes certain knowledge of > Informatics. For instance, how do I launch Modeller? From the prompt > of a OS terminal? There are many other resources available for learning informatics, and it's really outside the scope of the Modeller tutorial to rehash them. There is a step-by-step guide to installing and using Modeller itself in the release notes at http://salilab.org/modeller/release.html You will also find running instructions in the manual at http://salilab.org/modeller/manual/node15.html To summarise these notes: for Windows, the installer adds a "Modeller" shortcut to your Start Menu, which opens a terminal for you. For Mac, you need to open the Terminal application. Then you just type 'mod8v1' and the name of your input file to run Modeller. > How to say to the program where my files are located? As with any other program, the files are in the directory which you run 'mod8v1' in, unless you give a full path name. See step 2 at that page in the manual I mentioned above. For PDB files, you may have them in a different directory, in which case it's useful to set the env.io.atom_files_directory variable. See the example in the manual. > Is there any basic, basic, basic (something like Modeller for Dummys > - as I am) tutorial to start with? I will very appreciate your help. I'm really not sure how the manual example could be any more straightforward, so if there are still points that aren't clear, feel free to follow up with me directly. > Also, any Spanish people working with Modeller? If anybody wants to add Spanish pages (in fact, pages in any language) for other Modeller users, there is a user-editable wiki available at http://salilab.org/modeller/wiki/ 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: 4 Date: Tue, 6 Sep 2005 10:33:13 +0200 From: Karsten Suhre Subject: Re: [modeller_usage] Tutorial for beginners? To: modeller_usage(a)salilab.org Message-ID: <200509061033.13904.karsten.suhre(a)igs.cnrs-mrs.fr> Content-Type: text/plain; charset="iso-8859-1" On Monday 05 September 2005 19:12, Modeller Caretaker wrote: > > Is there any basic, basic, basic (something like Modeller for Dummys > > - as I am) tutorial to start with? I will very appreciate your help. > > I'm really not sure how the manual example could be any more > straightforward, so if there are still points that aren't clear, feel > free to follow up with me directly. You might try "Bioinformatics for Dummies" ... http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0764516965,page-1.ht… Kind regards, Karsten. ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 4, Issue 75 ********************************************* __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com >P1;2PIA StructureX:2PIA :8: :320: :Oxido:HUM: : FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW------------- ------------------------------------------------------------- ------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD* >P1;1GVH StructureX:1GVH :212: A :261:A :oxido:uk2: : ------------------------------------------------------------P D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TVC StructureX:1TVC :44:A:248:A :oxidored:uk3: : ---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL----------------------- ------------------------------------------------------------- ----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF FEKF---LPSG-------------------------------------------------- ------------------------------------------------------* >P1;1KRH StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------* >P1;2CND StructureX:2CND :145: :257: :oxidored:uk5: : ------------------------------------------------------------- -----------------------------------------------------------GS GITPMYQIIQAVLRDQPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQV KRPEEGWKYSVGFV-TEAVLREHVPEGGDDTLALACGPPPMIQFAISPNLE---------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1QGA StructureX:1QGA :194:B :231:B :oxidored:uk6: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE Q------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------* >P1;1H42 StructureX:1H42 :190:A :235:A :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE QKNPQ--GGR--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1FNC StructureX:1FNC :234: :281: :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------SRE QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI--------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1RFK StructureX:1RFK :4: B :91:B :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET* >P1;reduct Sequence:reduct:1 : :344 : :hypo:unknown: : FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD* # A sample TOP file for fully automated comparative modeling INCLUDE # include MODELLER routines SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files SET ALNFILE = 'alignm.ali' # input file w/ templates and target SET KNOWNS = '2PIA' '1GVH' '1TVC' '1KRH' '2CND' '1QGA' '1H42' '1FNC' '1RFK' # templates' PDB codes SET SEQUENCE = 'reduct' # target code SET STARTING_MODEL = 1 SET ENDING_MODEL = 3 SET HETATM_IO = ON SET OUTPUT_CONTROL = 1 1 1 1 1 CALL ROUTINE = 'model' # get alignment and a model

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What I'm doing wrong?
by Antonio Arroyo Luque 08 Sep '05

08 Sep '05

Hello Everyone, I'm trying to follow the tutorial. And this is what I get. Any help? Thank you Antonio Arroyo Note: Translation at the end is added by myself. *************************************************************************** Type 'mod8v1 model-default.py' to run Modeller on the script 'model-default.py'. F:\Archivos de programa\Modeller8v1>mod8v1 model-default.py FATAL ERROR: Cannot open file model-default.py: No such file or directory F:\Archivos de programa\Modeller8v1>c: C:\>cd basic-example C:\basic-example>dir El volumen de la unidad C es Esclavo El número de serie del volumen es: 9013-03E9 Directorio de C:\basic-example 08/09/2005 10:37 <DIR> . 08/09/2005 10:37 <DIR> .. 10/06/2005 17:03 246.159 1b8p.pdb 10/06/2005 17:03 453.033 1bdm.pdb 10/06/2005 17:03 142.581 1bdmA.profile 10/06/2005 17:03 3.198 1bdmA_dope.dat 10/06/2005 17:03 277.749 1civ.pdb 10/06/2005 17:03 1.606.878 1smk.pdb 10/06/2005 17:03 500.477 5mdh.pdb 10/06/2005 17:03 970.763 7mdh.pdb 10/06/2005 17:03 2.940 align2d.log 10/06/2005 17:03 349 align2d.py 10/06/2005 17:03 11.927 build_profile.ali 10/06/2005 17:03 16.593 build_profile.log 10/06/2005 17:03 13.540 build_profile.prf 10/06/2005 17:03 1.252 build_profile.py 10/06/2005 17:03 122.300 compare.log 10/06/2005 17:03 236 compare.py 10/06/2005 17:03 17.178 dope_evaluation.pdf 10/06/2005 17:03 180.013 evaluate_model.log 28/06/2005 10:38 890 evaluate_model.py 10/06/2005 17:03 167.409 evaluate_template.log 28/06/2005 10:37 860 evaluate_template.py 10/06/2005 17:03 215 family.mat 06/09/2005 10:08 1.483 model-default.log 06/09/2005 11:00 68.299 model-single.log 10/06/2005 17:03 193 model-single.py 10/06/2005 17:03 5.063.163 pdb_95.pir 10/06/2005 17:03 819 TvLDH-1bdmA.ali 10/06/2005 17:03 1.538 TvLDH-1bdmA.pap 10/06/2005 17:03 383 TvLDH.ali 06/09/2005 10:47 213.789 TvLDH.B99990001.pdb 06/09/2005 10:51 213.789 TvLDH.B99990002.pdb 06/09/2005 10:54 213.789 TvLDH.B99990003.pdb 06/09/2005 10:57 213.789 TvLDH.B99990004.pdb 06/09/2005 11:00 213.789 TvLDH.B99990005.pdb 06/09/2005 10:46 24.990 TvLDH.D00000001 06/09/2005 10:50 25.305 TvLDH.D00000002 06/09/2005 10:53 25.620 TvLDH.D00000003 06/09/2005 10:56 25.200 TvLDH.D00000004 06/09/2005 10:59 25.410 TvLDH.D00000005 06/09/2005 10:44 213.733 TvLDH.ini 10/06/2005 17:03 150.163 TvLDH.profile 06/09/2005 10:44 2.188.086 TvLDH.rsr 06/09/2005 10:57 3.121 TvLDH.sch 06/09/2005 10:47 150.529 TvLDH.V99990001 06/09/2005 10:51 150.529 TvLDH.V99990002 06/09/2005 10:54 150.529 TvLDH.V99990003 06/09/2005 10:57 150.529 TvLDH.V99990004 06/09/2005 11:00 150.529 TvLDH.V99990005 10/06/2005 17:03 3.351 TvLDH_dope.dat 49 archivos 14.378.987 bytes 2 dirs 53.856.186.368 bytes libres C:\basic-example>>P1;TvLDH "TvLDH" no se reconoce como un comando interno o externo, [Translation: "TvLDH" is not recognized as either an internal or external command, programa o archivo por lotes ejecutable. program or a batch-script file] Sorry if not well translated C:\basic-example> *******************************************************************

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Nucleic acid-protein complexe
by Charlotte Habegger-Polomat 07 Sep '05

07 Sep '05

Hello! This is a question I posted a while back with no answer. I'm trying again in hopes that this is the right spot and that someone can help me out with this! I have successfully modelled a protein using Modeller with three template structures from the PDB. I now would like to add on a tRNA which is present in other homologous structures in the PDB. Must I redefine nucleic acids in the Modeller files or should Modeller be able to recognize common nucleic acid "residues"? Any suggestions as to how to obtain a quick first model of the complex will be greatly appreciated! Thank you! -Charlotte Habegger-Polomat

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Tutorial for beginners?
by Antonio Arroyo Luque 06 Sep '05

06 Sep '05

Hello everyone, I try to lunch and run Modeller8v1 without any success. I use either the Windows or the Mac version of the program. The problem I have is that I don't know anything about Informatics but I want to learn. The tutorial of Modeller I've found assumes certain knowledge of Informatics. For instance, how do I launch Modeller? From the prompt of a OS terminal? How to say to the program where my files are located? I have this problem since version 6 of Modeller (more than 2 years ago) and since that I've been downloading new versions of the program but as I said without any success. Is there any basic, basic, basic (something like Modeller for Dummys - as I am) tutorial to start with? I will very appreciate your help. Also, any Spanish people working with Modeller? Thank you very much Antonio

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Internal error: array too small
by hchoe 01 Sep '05

01 Sep '05

Dear Modeller, I've got this error message. dihdisn_223E> Internal error: array too small: current maximum, current need: 100 101 What should be fixed? Thanks in advance.. Cheers, Han

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profile files
by Jason M Walraven 01 Sep '05

01 Sep '05

How can I view a graph of the evaluate_model.py profile files? An example graph is given in the tutorial, but no info on how to view it in graphical form. Do I manually transfer the DOPE score values from the file to a graphing program, or is there an easier way? Thanks!

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