- modeller_usage - salilab.org

How analyse "model_segment"
by li bai 07 Aug '06

07 Aug '06

Dear, everyone! Could you tell how analyse like: model_segment=('FIRST:A','LAST:A') model_segment=('FIRST:@,'END:') model_segment=('2','50') model_segment=('!2','!50') Could give me an answer? Thank you very much! Sincerely! Yours, --------------------------------- Mp3疯狂搜-新歌热歌高速下

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Help:analyse .profile
by li bai 06 Aug '06

06 Aug '06

Dear,everyone! How do I analyse a plot of .profile in the 'basic tutorial'? It says 'This profile is written to a file `TvLDH.profile', which can be used as input to a graphing program such as GNUPLOT', but when a plot it ,I get a straight line.How do I analyse it???What does mean? Does it sense?Thank you! Sincerely --------------------------------- 雅虎免费邮箱-3.5G容量，20M附件

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Help :How I get dop.dat
by li bai 06 Aug '06

06 Aug '06

Hello,TvLDH_dope.dat Everybody! When I do baisic-example ,I find "TvLDH_dope.dat". But I do not know how get it! Who can tell me how I can get it ? Thank you! Sincerely! --------------------------------- 雅虎免费邮箱-3.5G容量，20M附件

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[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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