- modeller_usage - salilab.org

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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applying symmetry
by Christian Meesters 23 Aug '07

23 Aug '07

Hoi, First of all, thanks for your last explanation, Ben (was: 'code and logic question'). I just forgot to reply. My problem now is, how to create and apply arbitrary symmetry: The manual provides the nodes 28 and 103- http://www.salilab.org/modeller/manual/node28.html http://www.salilab.org/modeller/manual/node103.html - which already is a good starting point, but even after looking into the python code it is not clear to me how to distinguish between different symmetries. How, for example would I have to write: "Add restraints for a model with D6 symmetry (Schönflies notation), where all subunits have identical sequences."? Or "add restraints for a hexameric model with C3 symmetry."? Are there examples beyond the two nodes which address this question? TIA Christian

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help--model_ini.py
by jinlian05＠lzu.cn 23 Aug '07

23 Aug '07

Hi: My initial model is one chain, I use model_ini.py scripts to build model, and edit my alignment file to add a starting residue number, such as: sequence:bhro:1::348:::::0.00:0.00 it also appears errors: 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 " ", chain " " now, how does MODELLER solve it? thank you!

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Reg. align_codes error in profile_build.py in Mod9v2
by saravanan 23 Aug '07

23 Aug '07

Please help me to rectify the error in mod9v2 My script from modeller import * log.verbose() env = environ() #-- Prepare the input files #-- Read in the sequence database sdb = sequence_db(env) #sdb.read(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.pir', seq_database_format='PIR',chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True) #-- Write the sequence database in binary form #sdb.write(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.bin', seq_database_format='BINARY', chains_list='ALL') #-- Now, read in the binary database sdb.read(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.bin', seq_database_format='BINARY', chains_list='ALL') #-- Read in the target sequence/alignment aln = alignment(env) aln.append(file='p17787.fas', alignment_format='FASTA', align_codes='p17787') #-- Convert the input sequence/alignment into # profile format prf = aln.to_profile() #-- Scan sequence database to pick up homologous sequences 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) #-- Write out the profile in text format prf.write(file='build_profile.prf', profile_format='TEXT') #-- Convert the profile back to alignment format aln = prf.to_alignment() #-- Write out the alignment file aln.write(file='build_profile.ali', alignment_format='PIR') aln.check() error what i have got 'import site' failed; use -v for traceback Traceback (most recent call last): File "build_profile.py", line 21, in ? aln.append(file='p17787.fas', alignment_format='FASTA', align_codes='p17787' ) File "C:\Program Files\Modeller9v2\modlib\modeller\alignment.py", line 74, in append rewind_file, close_file) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = p17787 ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Re: [modeller_usage] Reg. comparing dope profile or both template and model
by saravanan 22 Aug '07

22 Aug '07

Now, we generated dope plot for template and model individually. How to visualize dope plot of both template and model in a single plot as mentioned in the basic tutorial.. Looking forward for reply... ---P.Saravanan ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/

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Reg. comparing dope profile or both template and model
by saravanan 22 Aug '07

22 Aug '07

Thanks for the help to generate dope plot. Now, we generated dope plot for template and model individually. How to compare dope plots of them in a single plot? looking forward for reply.. P.Saravanan SRF Dept. of PharmacoInformatics NIPER INDIA ____________________________________________________________________________________ Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7

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help--model_ini.py
by jinlian05＠lzu.cn 22 Aug '07

22 Aug '07

Hi: When I use my initial model to build the structure, it appears some erros, the following is the scripts and log file: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'bhro_mult.ali', knowns = ('bhro_n','bhro_tm','bhro_c'), sequence = 'bhro', inifile = 'myini.pdb') a.starting_model= 1 a.ending_model = 1 a.make() some errors in log file: 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 " ", chain " " read_te_288W> Protein not accepted: 1 myini.pdb rdabrk__337E> Structure not read in (please consult the log file for more details): now, how does MODELLER to do this question? thanks a lot!

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Re: [modeller_usage] Secondary Structure Restraints
by Modeller Caretaker 21 Aug '07

21 Aug '07

Victoria Ann McKenna wrote: > If I was trying to restrain the secondary structure of the > target but in some instances this differs from the > secondary structure of the template, how would MODELLER > restrain, or over ride the restraints of the target (i.e. > how does it choose which restraints to use and when?). Modeller always uses all restraints, so there is no choice to be made here. If you are worried about user-supplied restraints conflicting with the default homology-derived restraints, you can weaken or remove the latter. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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align sequences
by rgerber2＠bigred.unl.edu 21 Aug '07

21 Aug '07

Hi, I have several proteins (AA sequences) that I would like to compare for possible interactions but I do not know where they will bind. I looked at the example: proteinA; AAAAAAAAAAAAA------------ proteinB; -------------BBBBBBBBBBBB chimera; AAAAAAAAAAAAABBBBBBBBBBBB but this didn't help as I don't know where they will interact/bind. I've tried a few times to enter the sequences, but obviously am getting error messages for incorrect format. Wondering if anyone knew how to solve this??? Thanks for your help, rgerber

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help--orient multiple template
by jinlian05＠lzu.cn 21 Aug '07

21 Aug '07

Hi: I use multiple templates to model target protein, those templates have no overlap, how does MODELLER to determine the orientation of multiple templates? There is no information about orientation restraint on target or template.

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