modeller_usage August 2007

modeller_usage@salilab.org

22 participants
49 discussions

Loop refinement
by ESTER FUSTE DOMINGUEZ 30 Aug '07

30 Aug '07

Dear Sir/madam, I built a model of a protein using Modeller, and with the PDB file obtained, I'm trying to model loops. I follow the online manual instructions "refining an existing PDB file". However, when I run mod9v2 I obtain this error:( "No such residue: %s" % indx ) Key Error: no such residue 266. In the logfile I don't see what is wrong, and in PDB file 266 residue exists, this is why I don't understand the error "no such residue 266". And could I model three loops at the same time? Thanks. Ester ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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platform (in)dependent libraries?
by Mike White 28 Aug '07

28 Aug '07

Hi there, I am running Modeller 9v2 on a 64-bit Linux (Suse) box, and when I ran a small test program, it ran fine (as evidenced from the results and log file), but I received the following errors: ******************************************************************** mike@linux-8h71:~/Modelling_projects/Test_Mod9v2> mod9v2 MakePAPFile.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback ******************************************************************* This may have something to do with the directories that various things are in. mod9v2 lives in usr/bin/ the actual programs reside in usr/lib/modeller9v2/ and Python (2.3, 2.4, and 2.5) live in usr/lib64/ Two questions: (1) Is this error something to worry about? (2) If so, how do I correct this problem? As you can guess from the questions, I'm still feeling my way around Linux Thanks Mike White

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multiple-template no overlap
by jinlian05＠lzu.cn 28 Aug '07

28 Aug '07

Hi: My target protein is a member of GPCR.I used multiple template to build the model, there was no overlap among the templates. The final model was not reasonable. The C-tail and N-tail were away from transmember region, simultaneity,located flank of transmember region.I want to know, was there any restraints on 'MODELLER'? the following is alignment: >P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbb---------* >P1;proteinC structureX:proteinC -----------------------------------------------------ccccccccc* >P1;model sequence:model aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbcccccccccc* The following was my script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='model_mult.ali', knowns=('proteinA','proteinB', 'proteinC' ), sequence='model') a.starting_model = 1 a.ending_model = 1 a.make() was I missing something important? Or, did it in a wrong way? looking for your reply! thanks!

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Problem when reconstruct the protein with know structure!
by liu xin 28 Aug '07

28 Aug '07

Hi all I divided the protein with know structure (bovine rhodopsin receptor) into three part: N-terminus region, transmembrane region and C-terminus region without change their initial coordinates, and I try to use the three parts to reconstruct the original structure of the protein. First, I aligned the three parts as the following way: (sorry, last letter I submited a wrong alignment,the following is I used) >P1;N-terminus structureX:N-terminus aaaaaaaaaa------------------------------* >P1;tm-region structureX:tm-region ----------bbbbbbbbbbbbbbbbbbbb----------* >P1;C-terminus structureX:C-terminus ------------------------------cccccccccc* >P1;original sequence:original aaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb* then I used the following script to generate the original structure of my protein: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='bhro_mult.ali', knowns=('bhro_n','bhro_tm','bhro_c'), sequence='bhro') a.starting_model = 1 a.ending_model =1 a.make() However, the generated model was different from the original one, looking closely, I found the difference mainly occurred in the N-terminus and C-terminus regions, their coordinates have changed greatly when compared with the original structure. I was missing something important? Or, did it in a wrong way? I am new to modeller, any suggestions are appreciated! Thanks in advance yours Xin Liu

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Problem when reconstruct the protein with know structure!
by liu xin 28 Aug '07

28 Aug '07

Hi all I divided the protein with know structure (bovine rhodopsin receptor) into three part: N-terminus region, transmembrane region and C-terminus region without change their initial coordinates, and I try to use the three parts as multiple templates to reconstruct the original structure of the protein. First, I aligned the three parts as the following way: N-terminus> aaaaaaaaa-------------------------------------* transmembrane> ----------------bbbbbbbbbbbbb---------------* C-terminus> --------------------------------------ccccccccc* original> aaaaaaaaabbbbbbbbbbbbbccccccccc* then I used the following script to generate the original structure of my protein: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='bhro_mult.ali', knowns=('bhro_n','bhro_tm','bhro_c'), sequence='bhro') a.starting_model = 1 a.ending_model =1 a.make() However, the generated model was different from the original one, looking closely, I found the difference mainly occurred in the N-terminus and C-terminus regions, their coordinates have changed greatly when compared with the original structure. I was missing something important? Or, did it in a wrong way? I am new to modeller, any suggestions are appreciated! Thanks in advance yours Xin Liu

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Modeling a sequence based on a low identity to a template
by ESTER FUSTE DOMINGUEZ 27 Aug '07

27 Aug '07

Dear Sir/Madam, I'm trying to model a sequence based on a low identity template. QUESTION 1: I follow the example "difficult modeling" from Modeller tutorial. However, in the last step, when I run "mod9v2 model.py" I obtain this misake described below: <<'import site' failed; use -v for traceback Traceback (most recent call last): File "model.py", line 9, in ? a.make() File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel py", line 99, in make self.homcsr(exit_stage) File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel py", line 412, in homcsr self.check_alignment(aln) File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel py", line 394, in check_alignment aln.check() File "C:\Archivos de programa\Modeller9v2\modlib\modeller\alignment.py", line 182, in check libs=self.env.libs.modpt) _modeller.error: read_te_291E> Sequence difference between alignment and pdb :>> I tried to solve it, but I could'nt. Could you help me, please? mGenTHREADER PREDICTION RESULTS: HTML formatted results can be found here: http://bioinf2.cs.ucl.ac.uk/psiout/d83ffff39d5b753b.mgen.html QUESTION 2: When my sequence was submitted to the mGenThreader server to fold assignment, the server didn't returned me any significat hit, all confidence levels were GUESS (p-value >= 0.1) Then, which hit should I take? The hit which have the smallest p-value or the hit with the highest percentage identity? Or maybe If I don't have any significat hit, all models built by MODELLER will be wrong.Is that true? QUESTION 3: In "difficult example" in MODELLER's tutorial, in this alignment, I don't know which is the criterion to choose 30 :A: 209 :A:::: in structureX. How do you count it? I don't undestand the way you count it. <<Alignment between the nsp16 sequence and the 1ej0A from mGenThreader results. C; mGenThreader alignment of 30133975 and 1ej0A C; CERT significance with an e-value of 1e-04 C; Percentage Identity = 14.4% >P1;1ej0A structureX:1ej0: 30 :A: 209 :A:::: -------GLRSRAWFKL----------------------------------DEIQQSDKLFKPGMTVVDL GA------APGGWSQYVVTQIGGKGRIIACDLLPMDPIVGVDFLQGDFRDELVMKALLERVGDSKVQVVM SDMAPNMSGTPAVDIPRAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSLFTKVKVRKPDS SRARSREVYIVATGRKP* >P1;30133975 sequence::::::::: ASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHF GAGSDKGVAPG--TAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVH----------TANKWDLII SDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHS-WNADLYKLMGHFSWWTAFVTNV NA-SSSEAFLIGANYLG* File 30133975_1ej0A_mGenThreader.ali. Red residues were manually removed from the alignment>> Thank you very much. Ester ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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ERROR MESSAGE
by ESTER FUSTE DOMINGUEZ 26 Aug '07

26 Aug '07

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ligand modeling in binding site of protein
by mahendra awale 24 Aug '07

24 Aug '07

hi i am doing ligand modelling in binding site of protein i am using script ligand/multiple-hetero.py as u specified in tutorial but getting error pdb files read when i run script but it shows errors when doing add_restraints that "one or more atoms absent from model" below is the error file after running this script Traceback (most recent call last): File "ligand.txt", line 17, in ? a.make() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 342, in homcsr self.mkhomcsr(aln) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 399, in mkhomcsr self.special_restraints(aln) File "ligand.txt", line 8, in special_restraints rsr.add(atom_ids=ids, restraint_parameters=(2,1,1,22,2,2,0,3.5,0.1)) File "/usr/local/modeller8v2/modlib/modeller/model.py", line 409, in add return self.top.add_restraint('restraints.add', mdl=self.__mdl.modpt, File "/usr/local/modeller8v2/modlib/modeller/util/top.py", line 329, in add_restraint return _modeller.add_restraint(mdl, *args) _modeller.error: add_res_442E> One or more atoms absent from MODEL: N1:101 N3:13 also shown below is log file check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 95 1 2 113 94 Q S 6.894 204 1 2 222 203 R F 6.290 230 1 2 248 227 P W 7.467 233 1 2 251 230 S V 7.787 END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 19 293 atom names : C +N atom indices : 2385 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 19 293 atom names : C CA +N O atom indices : 2385 2374 0 2386 omgdel__425W> Unselected all O C +N +CA dihedrals: 306 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. iup2crm_279W> IUPAC atom not found in topology library; residue type index: OD1 2 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: OD2 2 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. add_res_442E> One or more atoms absent from MODEL: N1:101 N3:13 please tell me what to do? thank u Mahendra Eknath Awale Institute Scholar M. S. (Pharm.) Dept.of Pharmacoinformatics National Institute of Pharmaceutical Education and Research NIPER S.A.S.Nagar, Mohali, Punjab-160062 INDIA. Institute Web http://www.niper.gov.in/ --------------------------------- Download prohibited? No problem. CHAT from any browser, without download.

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ligand modeling in binding site of protein
by mahendra awale 24 Aug '07

24 Aug '07

hi i am doing ligand modeling in protein active site i run ligand/multiple-hetero.py script but geting errors it reads the pdb file but at the restraints line it shows one or more atoms not found in model Mahendra Eknath Awale Institute Scholar M. S. (Pharm.) Dept.of Pharmacoinformatics National Institute of Pharmaceutical Education and Research NIPER S.A.S.Nagar, Mohali, Punjab-160062 INDIA. Institute Web http://www.niper.gov.in/ --------------------------------- Get the freedom to save as many mails as you wish. Click here to know how.

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ligand modeling in binding site
by mahendra awale 23 Aug '07

23 Aug '07

Hi i am doing ligand modeling in binding site of protein i am using ligand/model-multiple-hetero.py script file but geting errors it is say that alignment sequence not found in pdb file the outpu after running script shown below File "ligand.txt", line 17, in ? a.make() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/local/modeller8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/usr/local/modeller8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/local/modeller8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: rdpir___648E> Alignment sequence not found in PDB file: 2 1xxx.pdb the log.file out put shown below rdpir___377W> Too many fields ( 11 - should be 10) in the second line of the sequence entry (fields are separated by a colon, :) structure:1GZ8.pdb::::::::0.00:00 rdpir___648E> Alignment sequence not found in PDB file: 2 1GZ8.pdb thank u Mahendra Eknath Awale Institute Scholar M. S. (Pharm.) Dept.of Pharmacoinformatics National Institute of Pharmaceutical Education and Research NIPER S.A.S.Nagar, Mohali, Punjab-160062 INDIA. Institute Web http://www.niper.gov.in/ --------------------------------- Once upon a time there was 1 GB storage in your inbox. Click here for happy ending.

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modeller_usage August 2007