September 2005 - modeller_usage

Re: [modeller_usage] sequence alignment of pdb file with missing residues]
by Charlotte Habegger-Polomat 22 Sep '05

22 Sep '05

Hello! Here is what I've tried for my protein's Cterm which did not align with any of my templates: 1- 2D structure prediction using only algorithms with at least 75% overall accuracy as determined monthly by EVA (http://salilab.org/~eva/) and using a consensus of all results as my final prediction 2 - This confirmed that the Cterm domain was probably all alpha since all proteins of known structure in this family of proteins have an all-alpha Cterm 3 - I then used the following script (it's an old .top file - there may be a new example using Python in the Modeller FAQ) for Modeller to set restraints for those last residues that were not aligned against any of the templates: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'alignment.ali' SET KNOWNS = 'xxx' 'xxx' 'xxx' SET SEQUENCE = 'xxxxxx' SET ATOM_FILES_DIRECTORY = '/xxx/xxxxxxx/xxxxxx/xxxx/' SET STARTING_MODEL = 1 SET ENDING_MODEL = 20 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '461' '465' RETURN END_SUBROUTINE -Charlotte Habegger-Polomat Lucas Bleicher wrote: >--- Charlotte Habegger-Polomat ><chpoloma(a)rsvs.ulaval.ca> a écrit : > > > >>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. >> >> > >That's an interesting approach - I always cut the >terminals of my modeled sequences when I have nothing >that align with it. If it's not asking much, could you >provide an example of how to do this in Modeller? > >Thanks in advance, >Lucas > > > > >___________________________________________________________________________ >Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger >Téléchargez cette version sur http://fr.messenger.yahoo.com > > >

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Problems with cis proline
by Eva María Priego 21 Sep '05

21 Sep '05

Dear all, I need to build models of a protien with a disulphide bond beetween monomers, four cis Proline and an aditional helix. I am using Modller 7v7. This is the top file I have used: INCLUDE SET ATOM_FILES_DIRECTORY ='/home/evamaria/CTLA-4/Dimer/Model9/' SET PDB_EXT = '.pdb' SET SEQUENCE = 'CTLA4-D' SET STARTING_MODEL = 1 SET ENDING_MODEL = 40 SET DEVIATION = 4.0 SET KNOWNS = '1i8lc' '1i8ld' '1i85cd' '1ah1a' '1ah1b' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET ALIGNMENT_FORMAT = 'PIR' SET ALNFILE ='CTLA4-D.ali' CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = 'on' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '127:' '149:' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '284:' '306:' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '122:' '279:' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:101' 'C:101' 'N:102' 'CA:102', ; ATOM_IDS2 = 'CA:101' 'C:101' 'N:102' 'CA:102' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:103' 'C:103' 'N:104' 'CA:104', ; ATOM_IDS2 = 'CA:103' 'C:103' 'N:104' 'CA:104' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:258' 'C:258' 'N:259' 'CA:259', ; ATOM_IDS2 = 'CA:258' 'C:258' 'N:259' 'CA:259' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:260' 'C:260' 'N:261' 'CA:261', ; ATOM_IDS2 = 'CA:260' 'C:260' 'N:261' 'CA:261' RETURN END_SUBROUTINE The problem is the models obtained don't fit this script, I mean, none of them have the alpha helix and none have the four correct cis proline( or have more residues in cis) but they have the disulphide bond.What am I doing wrong?. Thank you in advance

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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> > >

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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 > > >

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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

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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

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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

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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

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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

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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

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