August 2006 - modeller_usage

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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