- modeller_usage - salilab.org

Re: [modeller_usage] Repeating basic tutorial with my protein - stuck at malign3d step
by Charlotte Habegger-Polomat 21 Sep '05

21 Sep '05

Thank you for the help! I did find my template sequences in $(LIB)/CHAINS_all.seq and now the sequence information is correct. -Charlotte Habegger-Polomat P.S. I am forwarding to the Modeller discussion group in case this may be of help to someone else ...but not Guido Leoni wrote: > Hi > The env directory is the directory where your seq.files and your > structures are located. If they are in $(LIB)/CHAINS_all.seq ok. > The log file tells you that your the align codes and the codes in the > seq.files are not the same check it and make you sure that they are > coincident > I hope that I have helped > > 2005/9/16, Charlotte Habegger-Polomat <chpoloma(a)rsvs.ulaval.ca > <mailto:chpoloma@rsvs.ulaval.ca>>: > > Hello! > > I have redone the basic tutorial successfully with the example given, > and would now like to reproduce those same steps with my protein of > interest. In my working directory, I have the PDB files for the > structures I'm trying to align and the following compare.py file: > > ------------------------------------------------ > env = environ() > aln = alignment(env, file='$(LIB)/CHAINS_all.seq', > align_codes=('1n75', '1n77')) > aln.malign() > aln.malign3d() > aln.compare_structures() > aln.id_table() > env.dendrogram() > --------------------------------------------------- > > > I was not sure what $(LIB)/CHAINS_all.seq referred to. > > If I need to change that line: > > aln = alignment(env, file='$(LIB)/CHAINS_all.seq', > > Then what type of file should I use? > > > This is the error message I am getting: > > ----------------------------------------------------- > File "compare.py", line 3, in ? > align_codes=('1n75', '1n77')) > File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py", > line 19, in __init__ > self.__int_append('alignment.append ', io, libs, vars) > File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py", > line 68, in __int_append > libs=libs.modpt, **vars) > File "/usr/local/packages/modeller8v1/modlib/modeller/util/top.py", > line 33, in read_alignment > return _modeller.read_alignment(aln, io, libs, *args) > _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was > not found in the alignment file; ALIGN_CODES( 1) = 1n75 > ---------------------------------------------------- > > and my compare.log: > > ------------------------------------------------- > Kind, OS, HostName, Kernel, Processor: 4, Linux pelican > 2.6.7-gentoo-r11 > i686 > Date and time of compilation : 06/20/2005 12:04:54 > MODELLER executable type : i386-intel8 > Job starting time (YY/MM/DD HH:MM:SS): 2005/09/16 11:37:06.955 > > read_al_373E> Protein specified in ALIGN_CODES(i) was not found > in the alignment file; ALIGN_CODES( 1) = 1n75 > --- > ----------------------------------------------- > > Thank you for any suggestions as to how I can compare the structures! > > -Charlotte > > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org <mailto:modeller_usage@salilab.org> > http://salilab.org/mailman/listinfo/modeller_usage > <http://salilab.org/mailman/listinfo/modeller_usage> > >

1 0

Re: [modeller_usage] sequence alignment of pdb file with missing residues]
by Charlotte Habegger-Polomat 21 Sep '05

21 Sep '05

Andy, There may be a better answer but depending on the length of the gaps where structure information is lacking, you could use 2D structure prediction programs for those regions and then impose certain restraints on Modeller. For example, the last 10 residues in my protein of interest did not have anything to align with in the sequences of the 4 templates. Using 2D structure predictions (I used EVA to choose the best performing programs: http://salilab.org/~eva/sec/res_sec.html) it was noted that this was most likely a helical structure, and I then used restraints suggesting to Modeller to use this type of structure for this part of the protein. Otherwise, without the restraints, I got various structural possibilities for the Cterm. In your case, you also have the alignment, so that should make it easier. Hope this can help or that someone else will have a better idea. -Charlotte Habegger-Polomat Andy Arvai wrote: >Hi, > >I'm a new user to modeller and I would like to do a sequence alignment >to a known structure which has gaps in the pdb file. The alignment >works with align2d, however the sequence of the missing residues in the >pdb file is not used. Ideally I would like to use the pdb file and the >full sequence (including the residues which are missing in the pdb >file). I know I can do an alignment of two sequences, but I'm wondering >if it would be possible to get the best of both worlds - using sequence >and structural information from the pdb file and also sequence >information from the missing gaps. I've tried putting the entire >sequence at the start of the pdb file with the SEQRES pdb keyword, but >this seems to be ignored. Thanks for any help. > >Andy > >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >http://salilab.org/mailman/listinfo/modeller_usage > > >

1 0

sequence alignment of pdb file with missing residues
by Andy Arvai 19 Sep '05

19 Sep '05

Hi, I'm a new user to modeller and I would like to do a sequence alignment to a known structure which has gaps in the pdb file. The alignment works with align2d, however the sequence of the missing residues in the pdb file is not used. Ideally I would like to use the pdb file and the full sequence (including the residues which are missing in the pdb file). I know I can do an alignment of two sequences, but I'm wondering if it would be possible to get the best of both worlds - using sequence and structural information from the pdb file and also sequence information from the missing gaps. I've tried putting the entire sequence at the start of the pdb file with the SEQRES pdb keyword, but this seems to be ignored. Thanks for any help. Andy

1 0

Error on Alpha Unix
by Ricardo Nicoluci 15 Sep '05

15 Sep '05

Hi, my name is Ricardo and I am trying to run Modeller version 8v1 on a Alpha System with Tru64 Unix and I am getting the following error: mod8v1: Cannot allocate space for bss. Killed Any susgestion !? Thanks, -- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil

2 2

question about basic modelling
by Mehmet Serkan Apaydin 14 Sep '05

14 Sep '05

Hi, I am a new MODELLER user. I am trying to duplicate a result in literature using v8.1 of MODELLER, and am trying to use 1H8C.pdb as template to model 1D3Z.pdb structure. I followed the basic outline of the scripts in the tutorial (and attached the scripts I used). At the end of modelling, the homology model I obtain is about 9A cRMSD from the target structure, whereas in the literature an earlier version of MODELLER (v6.2) was used to achieve a closer structure to the template (1.9A cRMSD). I was wondering whether there is any simple step I may be missing. Thanks, --Serkan

2 1

structure not read in
by sankari thirumal 13 Sep '05

13 Sep '05

Hi modellers, My protein sequence is aligned with the template sequence. I've done the alignment according to the psipred alignment. Hence i have to delete the first 40 residues in my protein seq to be modeled and 16 residues in the template sequence. The actual length of my sequence is 500 The actual lenth of template is 455 I have the following queries I have aligned the file in clustal and i'm getting only .aln file (in the pir format) and not .ali file Please tell me whether am i right? I have downloaded the pdb file and placed in the atom files folder. I have aligned the sequences as i said earlier and ranamed the file as apnew.ali put it in the automodel directory. I have also modified the model-defalut.py file and named as model-template.py Now my question is when i place the template file with full 455 residues, while 40 residues deleted in the alignment will it create some problems? and also tell me How to get the .ali file? This is the error message i recieve when i run the modeller, what to do ?can anyone help? C:\Program Files\Modeller8v1\examples\automodel>mod8v1 model-template.py Traceback (most recent call last): File "model-template.py", line 18, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li ne 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li ne 331, in homcsr aln.check() File "C:\Program Files\Modeller8v1\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in c heck_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in: 1 I have attached the log file, ali file and also the modified model-default.py file Thanks in advance sankari Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --------------------------------- # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'Apnew.ali', # alignment filename knowns = '1u13', # codes of the templates sequence = '1ptg') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling --------------------------------- _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'Apnew.ali', # alignment filename knowns = '1u13', # codes of the templates sequence = '1ptg') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling

1 0

structure not read in
by sankari thirumal 12 Sep '05

12 Sep '05

Hi modeller, My protein sequence is aligned with the template sequence. I've done the alignment according to the psipred alignment. Hence i have to delete the first 40 residues in my protein seq to be modeled and 16 residues in the template sequence. The actual length of my sequence is 500 The actual lenth of template is 455 I have the following quries I have aligned the file in clustal and i'm getting only .aln file (in the pir format) and not .ali file Please tell me whether am i right? I have downloaded the pdb file and placed in the atom files folder. I have aligned the sequences as i said earlier and ranamed the file as apnew.ali put it in the automodel directory. I have also modified the model-defalut.py file and named as model-template.py Now my question is when i place the template file with full 455 residues, while 40 residues deleted in the alignment will it create some problems? and also tell me How to get the .ali file? This is the error message i recieve when i run the modeller, what to do can anyone help? C:\Program Files\Modeller8v1\examples\automodel>mod8v1 model-template.py Traceback (most recent call last): File "model-template.py", line 18, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li ne 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", li ne 331, in homcsr aln.check() File "C:\Program Files\Modeller8v1\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in c heck_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in: 1 C:\Program Files\Modeller8v1\examples\automodel> regards san __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'Apnew.ali', # alignment filename knowns = '1u13', # codes of the templates sequence = '1ptg') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling

1 0

Building tetramers
by Cesar Luis Avila 12 Sep '05

12 Sep '05

Dear modeller comunity, I would like to know which is the best way to build a model of an homotetrameric protein from two or three templates. Is it preferable to build the monomer first and then assemble it in a posterior step or do I build the tetramer from the beginning? How may I align the tetrameric templates structures? Thanks for your help Cesar Avila Universidad Nacional de Tucuman Argentina ___________________________________________________________ 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo http://correo.yahoo.com.ar

1 0

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*

1 0

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

1 0