-- modeller-care@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@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@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@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@salilab.org Message-ID: 200509061033.13904.karsten.suhre@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.htm... Kind regards, Karsten. ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage@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