- modeller_usage - salilab.org

[Fwd: "bad ulimit" when running Modeller on solaris]
by Nicolas Fusseder 03 Aug '06

03 Aug '06

Hi, I would like to run modeller 8v2 on a Solaris OS version 5.9. I followed the installation instructions but upon running the program I encounter the following error: # mod8v2 ../examples/automodel/model-default.py /usr/bin/mod8v2: ulimit: bad ulimit /export/home/nickf/bin/modeller8v2/bin/mod8v2_sun4: syntax error at line 1: `(' unexpected Any ideas how to resolve this error? The ulimit on my machine is set to unlimimted. Could that error occur because the executable shell script is unable to obtain the current ulimit setting? Btw, I have Modeller running fine on Windows XP and Fedora. Any help would be greatly appreciated. -- Nicolas Fusseder La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037 USA

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secondary structures in homo trimers
by Prabhakar. G. 01 Aug '06

01 Aug '06

Dear Modeller Caretaker, am modeling a homo trimer, from a homo trimer template, each chain(A,B,C) in both template and query has 390 residues, no gaps in the sequence alignment, and sequence identity is 64%, but when the model is built , all the three chains in the models are not having same secondary structural in certain parts, eg: residues 15-24 is a strand in A chain and B chain but it is a coil in C chain. Is there a way to preserve the secondary structure in all the chains of the models? and why does this change of secondary structure happens? There are no such secondary structure variations as far as the template chains are concerned. thanks prabhakar

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I have errors in the build_profile() command, plx help me!
by Ngo Duc Tri 01 Aug '06

01 Aug '06

I'm reading the basic tutorial and practicing to model my own protein. My protein sequence is in the file ELI1537.ali (no gaps) : >P1;ELI1537 sequence:ELI1537:::::::0.00:0.00 MAGPSLGEWKAKAQHFAYDGLQIAFWTGGKPDARPLLLVHGYPTASWDWHRVWETLGSKY HLVAPDMIGFGLSDKPRSGYSIHRQADMHVALLDHLGIGAFDALVHDYGVSVGQELLARR AERSAAQGLGQAQDTTNGGIFPDQHRPRPIQKLGTSPLGFLVGLLTNREKFGRSFSEVFGP DTQPGAQELDEFWDLVSHNGGNRIMHKLLHYIADRKEHAERWFDALRIAQGDIGLINGAL DPVSGRHAYEAWRERLPDARHHLIPTVGHYPQVEDPQTVSRVTLDWLAR* The file build_profile.py is: from modeller import * log.verbose() env = environ() sdb = sequence_db(env) sdb.read(seq_database_file='pdb_95.pir', seq_database_format='PIR', chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True) sdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL') sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL') aln = alignment(env) aln.append(file='ELI1537.ali', alignment_format='PIR', align_codes='ALL') prf = aln.to_profile() prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat', gap_penalties_1d=(-500, -50), n_prof_iterations=1, check_profile=False, max_aln_evalue=0.01) prf.write(file='build_profile.prf') aln = prf.to_alignment() aln.write(file='build_profile.ali', alignment_format='PIR') I also copy the file pdb_95.pir to the current directory. I don't understand why there're errors that is: Traceback (most recent call last): File "build_profile.py", line 23, in ? aln.append(file='ELI1537.ali', alignment_format='PIR', align_codes='ALL') File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/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) = ALL Please help me to solve this error, I try to find answers in modeller forum but it's no use. Thank you very much! Best regards, NGODUCTRI

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handling missing residues in pdb files when doing multiple alignments
by Mike White 31 Jul '06

31 Jul '06

I am modeling a homopentamer in several different conformations using multiple templates as described in the Advanced tutorial. My modelling process involves using three different templates from homologous proteins and getting a structure-based alignment of the templates using salign. One of the templates has several gaps in the same position in each of the subunits (missing 1-3 amino acids in the structure).The resulting structure-based alignment doesn't show the missing residues as gaps of the proper length (this may be because the missing residues are in the middle of long loop without structure at subunit-subunit interfaces and one might be able to do without one or two residues here). I know that when one uses a single template with missing residues one should correct the alignment between the sequence to be modeled and the template by introducing gaps in the alignment for the missing residues. At what point would one deal with this when using multiple templates? If you insert the gaps in the structure-based alignment before aligning the sequence, are the gaps preserved, or do you then have to tweak the final alignment a bit more before modeling? I assume that the "adjustments are made in the Thanks Mike White

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I don't know how to get the file pdb_95.pir in my case, plz, tell me what to do.
by Ngo Duc Tri 31 Jul '06

31 Jul '06

Dear all, I'm newbie in Modeller so I practice the Tutorial (Basic Example 1). It's ok but when I model my protein, I don't know how we can obtain the file pdb_95.pir which contains sequences that are 95% identity to my protein? Which program or which command will I need to do? Can anyone help me? Thank you very much. With my best regards, TriNgo

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Error in "Unknown residue type, position, sequence" once more.
by Ngo Duc Tri 31 Jul '06

31 Jul '06

I'm sorry to disturb you but i got the old error say that: "read_al_375E> Unknown residue type,position,sequence" when I run the script: model-single.py. I also check the name very careful. It's right. Please tell me how to solve this error. Here is my code: File model-single.py: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='blbp-1ehyA.ali', knowns='1ehyA', sequence='blbp') a.starting_model = 1 a.ending_model = 5 a.make() File blbp-1ehyA.ali: >P1;1ehyA structureX:1ehyA: 2 :A: 294 :A::: 2.10:-1.00 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLND LSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFESWYSQFHQLDMAV EVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLP VTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR* >P1;blbp sequence:blbp::::::: 0.00: 0.00 MPDPASGIAI NRVPANGLEF EVAMAGEGDH LALMLHGFPE LHFSWRHQMP LLAEMGYRVW APNMRGYGET TRPTEVRDYA LDHLTQDVAA LIDASGATKV TLIAHDWGAI IAWYFAILKL RPLERLVIMN VPHPKVLQRE LRRWEQIKKS WYVFFFQLPW LPEKRIGADS GKRIGELFAQ TSCNPERFGP DVKAVYAAGA ARPGAPRAMV NYYRAAMRHR DTIDPGDFRV DVPTLLVWGE EDVALNIRCT EGTEQWVPDI TVKRLPNVSH WVQQDAPDEV NAILREWLPK PAPAS* Thank you very much!!! NgoDucTri

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[ help ] exceeded maxmol_pdf?
by Cathy Chang 26 Jul '06

26 Jul '06

Hi, I'm trying to model a protein that is about 890 aa long. I was provided with 1NW1 to model against; however, the problem I ran into was that the output structure from Modeller had a protein core and a long tail region. I ran my target in 123D+ and found 1JQI to align fairly well with this trailing tail region, so I want to model my target with both 1NW1 (core region - 32:A:426:A) and 1JQI (trailing tail region - 4:A:387:A). However, when I run Modeller, I get all of the output except the PDB file, and this error message keeps appearing in my log file: >> Summary of failed models: acad10.B99990001.pdb Obj. func. (164592.781) exceeded max_molpdf (100000.000) ==> (note: the obj. func. value changes but it's always over the max) I tried changing the domains of both 1NW1 and 1JQI, but I still get the same error message. How would I be able to avoid exceeding the max pdf size if I want to model my target with both of the listed proteins against the specific areas of my target? Thank you for your help! - Cathy

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[Modeler] Question about this alignment
by Hoffmann 26 Jul '06

26 Jul '06

Hello, I have generated several protein models with modeller, However, for the alignment shown before, I didn't suceed. What am I missing? structureX:1dkr:167:A:316:A:PDB::0.00:0.00 DIVIVSPDHGGVTRARKLADRLKAPIAIIDKRXXXXXXXXXMNIVGNIEGKTAILIDDIIDTA----GTITLAANALVENGAKEVYACCT-HPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLFS* >P1;pep sequence::::::SEQ::0.00:0.00 ------------------------------------AVADKRPRGRPRKHS-VISGQDFIEGGWVGWPEARQLAAALCQRRIP-CSVCLTKAVELGAPTDAFWLDPD-GVHCPLVPLRQRPTQRPVTLVSV------------------------* Thanks, Hoffmann __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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modelling fragments
by Viktor Hornak 25 Jul '06

25 Jul '06

Dear All, I was trying to use Modeller to produce coordinates of parts of a given target sequence based on full PDB coordinates of a template. For example: my template has a sequence AAAAABBCCCCCDDEEEEE which represents three helices (AAAAA, CCCCC, EEEEE) connected by two loops (BB, DD). My target has a sequence aaaaabbcccccddeeeee (again three helices and two loops) and I would like to overlap target helices on the template helices such that the loops in target are ignored. In other words, the resulting coordinates for the target would just have three helices (aaaaa, ccccc, eeeee). I have tried different alignment variants, such as: >P1;mol1 structureX:mol1:1: :19: : :2.2: AAAAABBCCCCCDDEEEEE* >P1;mol2 sequence:mol2: : : : : : : aaaaa--ccccc--eeeee* but the target sequence always wants to be connected; I don't know how to make Modeller to produce three helical fragments modeled on template helices of the full PDB structure. If some Modeller expert could provide advice or point out what I am doing wrong, I would greatly appreciate it... Thanks! -Viktor -- ===================== Viktor Hornak SUNY at Stony Brook =====================

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[ question ] atom files?
by Cathy Chang 21 Jul '06

21 Jul '06

Hi, My name is Cathy. I'm a new user of Modeller, and I'm still trying to figure out the input files to run Modeller. I'm having trouble with the atom files...I don't exactly know what is an atom file. I tried using the .pdb file straight from the PDB. I tried changing the file content to just the "atom" section of the PDB files. And nothing seems to work. I have the script file & alignment file in the default Modeller directory, and I set the atom file environment to a folder named "atom_files" with the 2 atom files (1pme & 1wbn). But when I try running my script, it says that atom files cannot be found in the directory atom_files. Here's the exact error message: ==================== Read the alignment from file : 1pme_1wbn.ali Total number of alignment positions: 388 # Code #_Res #_Segm PDB_code Name ---------------------------------------------------------------------------- --- 1 1pme 380 1 1pme 2 1wbn 360 1 1wbn runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL \Modeller8v2\atom_files\1pme.atm rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 0", chain " " rdabrk__288W> Protein not accepted: 1 1pme check_a_337E> Structure not read in (please consult the log file for more details): 1 1pme ==================== It would be great if anyone can help me with this problem! Thank you very much for your time! - Cathy

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