- modeller_usage - salilab.org

dope energy of template
by caj 18 Aug '06

18 Aug '06

Hi all, The evaluate-model.py was used for a few of my models but I would like to compare the DOPE energies to my template and where do I find that data-set? Hope it is not too obvious.... Best wishes Caroline

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enforcing symmetry in loop refinement
by Mike White 10 Aug '06

10 Aug '06

I have modeled a homopentamer using automodel with enforcing pentameric symmetry, and everything looks fine. There are two regions of each subunit that have 3 and 5 residue long loops that aren't in the templates. When I do loop modeling of all 10 of these loops at the same time using a script based on the one in the Advanced tutorial, I get a set of models where the loops are no longer symmetric. I then introduced the same symmetry constraints in the loop modeling that I used in the original model, and it produced models with the appropriate symmetry. However, it took much longer (765 seconds of cpu time to generate 5 loop models without the symmetry , but 8629 seconds to generate 2 loop models with symmetry). I don't mind letting things run overnight to generate models, but the hugh increase in computational time suggests that I might not be doing this right. Below is the python script: ******************************************************************* # Loop refinement of an existing model of the receptor from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' def defsym(mdl, aln, seg1, seg2): for (set,seg) in [(2,seg1), (3,seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set,selection_segment=seg, atom_types='ALL',selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0,add_symmetry=(True,False)) segsize = 217 #number of residues per chain # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 4 residue insertion in Loop C in each subunit self.pick_atoms(selection_segment=('198:', '201:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('415:', '418:'), selection_status='ADD') self.pick_atoms(selection_segment=('632:', '635:'), selection_status='ADD') self.pick_atoms(selection_segment=('849:', '852:'), selection_status='ADD') self.pick_atoms(selection_segment=('1066:', '1069:'), selection_status='ADD') # 3 residue insertion in Loop F in each subunit self.pick_atoms(selection_segment=('162:', '164:'), selection_status='ADD') self.pick_atoms(selection_segment=('379:', '381:'), selection_status='ADD') self.pick_atoms(selection_segment=('596:', '598:'), selection_status='ADD') self.pick_atoms(selection_segment=('813:', '815:'), selection_status='ADD') self.pick_atoms(selection_segment=('1030:', '1032:'), selection_status='ADD') def special_restraints(self, aln): #identify the seqments to maintain symmetry: A-B, B-C, C-D, D-E defsym(self,aln,seg1=('1',str(segsize)), seg2=(str(segsize+1),str(2*segsize))) defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)), seg2=(str(2*segsize+1),str(3*segsize))) defsym(self,aln,seg1=(str(2*segsize+1),str(3*segsize)), seg2=(str(3*segsize+1),str(4*segsize))) defsym(self,aln,seg1=(str(3*segsize+1),str(4*segsize)), seg2=(str(4*segsize+1),str(5*segsize))) m = myloop(env, inimodel='ReceptorBEST.pdb', # initial model of the target sequence='Receptor') # code of the target m.loop.starting_model= 11 # index of the first loop model m.loop.ending_model = 12 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() ******************************************************************************** The only difference between the two scripts is the inclusion of the definition of the defsym operation and the mdl.symmetry.define operation and the "def special_restraints" block. The cutting and pasting into this message screwed up the indentation, but the "mdl.symmetry.define" command is lined up with the "for (set, seg).." line. Have I done this right? I'm still at the "copying other scripts and trying to adapt them to my needs stage." There was an earlier post about this topic (http://salilab.org/archives/modeller_usage/2005/msg00381.html )but I didn't quite understand how this was to be implemented in loop modeling. Thanks! Mike White

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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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