- modeller_usage - salilab.org

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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Regarding violations profile
by harpreet singh 20 Aug '07

20 Aug '07

Dear Sir,I am running energy command in modeller with the parameters very_log, violations_profile and energy_profile in the log file I am getting very few violations in the "summary or restraints violations" , but when i see the the violations profile file the number of violations listed in this file are much more as compared to the violations mentioned in summary.Can you please help me understanding why there is duifference in violations shown in summary and that listed in the violations profile.RegardsHarpreet Singh _________________________________________________________________ Messenger Café — open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGLM_AugWLtagline

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Re: [modeller_usage] warning rectifications
by vidhya sankar 20 Aug '07

20 Aug '07

1) WHEN I RUN SUPEPOSE.py script i have got the follwing warninig how can i rectify readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 8 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 9 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 10 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 11 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 12 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 13 No more warnings will be printed for truncated lines in this file. 2)WHEN I RUN model_evaluate.py i have got the follwing warninig how can i rectify getf_______W> RTF restraint not found in the atoms list: residue type, indices: 5 529 atom names : C CA +N O atom indices : 4234 4226 0 4235 modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. loop optimization in the presence of a ligand (Thijs Beuming) 2. Re: loop optimization in the presence of a ligand (Modeller Caretaker) 3. Re: modeller_usage Digest, Vol 6, Issue 79 (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Thu, 16 Aug 2007 16:21:11 -0400 From: "Thijs Beuming" Subject: [modeller_usage] loop optimization in the presence of a ligand To: modeller_usage(a)salilab.org Message-ID: <5C60D3FA-2EF9-44A4-A613-BA0C09614F12(a)med.cornell.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, I am trying to optimize a loop in close proximity to a ligand. For some reason, the intial models have the ligand present, while the loop optimized models do not. Hence, there are major clashes between some of the calculated loops and the ligand. Is it possible to optimize loops in the presence of the ligand? My input script: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = 'MODELLER' class mymodel(loopmodel): def special_restraints(self, aln): rsr = self.restraints rsr.add(atom_ids=('CA:189', 'CA:372'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:189', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:372', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['176'], self.residues ['185'])) def select_loop_atoms(self): return selection(self.residue_range('378:', '383:')) a = mymodel(env, alnfile = 'MODELLER/alignment.pir', # alignment filename knowns = 'template', # codes of the templates sequence = 'target') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do the actual homology modeling Thanks, Thijs Beuming ------------------------------ Message: 2 Date: Thu, 16 Aug 2007 16:41:55 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] loop optimization in the presence of a ligand To: Thijs Beuming Cc: modeller_usage(a)salilab.org Message-ID: <46C4E0C3.5090904(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thijs Beuming wrote: > I am trying to optimize a loop in close proximity to a ligand. For > some reason, the intial models have the ligand present, while the > loop optimized models do not. Hence, there are major clashes between > some of the calculated loops and the ligand. Is it possible to > optimize loops in the presence of the ligand? It's hard to say for sure what your problem is without seeing all of your input files, but it looks like you haven't turned on env.io.hetatm, so I don't think you should be seeing ligands in either your regular models or your loop models. You can see the restraints that loopmodel builds by looking at the loop_restraints() method in the modlib/modeller/automodel/loopmodel.py file. By default it builds stereochemical, phi/psi, and dihedral restraints, but not the ligand-protein restraints that automodel does. You could easily fix this to restrain ligands by overriding the special_restraints() method and calling automodel.nonstd_restraints() from there. Note however that the ligand-protein restraints may be too strong to allow your loop to explore much conformational space, so it may make sense to use weaker or fewer restraints here. > def special_restraints(self, aln): > rsr = self.restraints > rsr.add(atom_ids=('CA:189', 'CA:372'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) > rsr.add(atom_ids=('CA:189', 'CA:393'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) > rsr.add(atom_ids=('CA:372', 'CA:393'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) Note that this way of specifying restraints is error prone and deprecated. You can see examples of the more robust method at http://salilab.org/modeller/9v2/manual/node209.html or http://salilab.org/modeller/tutorial/advanced.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Fri, 17 Aug 2007 06:25:46 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] modeller_usage Digest, Vol 6, Issue 79 To: modeller_usage(a)salilab.org Message-ID: <70610.83508.qm(a)web51610.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" can i compare th DOPE score of my mode with dope score of X-ray PDB.?if i can, what should be the DOPE SCORE difference between my model and X-ray PDB in order tobe my model is a reliable model. could you please tell some difference in score value yhanks in advance modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: superpose.py (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Thu, 16 Aug 2007 01:00:44 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] superpose.py To: modeller_usage(a)salilab.org Message-ID: <467087.77948.qm(a)web51604.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ? modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: log files (vidhya sankar) ---------------------------------------------------------------------- Message: 1 Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] log files To: modeller_usage(a)salilab.org Message-ID: <267539.63819.qm(a)web51610.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: DOPE (Modeller Caretaker) 2. regarding DOPE score (vidhya sankar) 3. regrding superpose.py (vidhya sankar) 4. ref: SUPERPOSE.PY (vidhya sankar) 5. Re: regarding DOPE score (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 09 Aug 2007 12:57:42 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] DOPE To: Ester Fust? Dom?nguez Cc: modeller_usage(a)salilab.org Message-ID: <46BB71B6.8070207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ester Fust? Dom?nguez wrote: > How can I see the DOPE score profile? I don't know how to use > *assess_dope* command. There is an example at the end of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT) From: vidhya sankar Subject: [modeller_usage] regarding DOPE score To: modeller_usage(a)salilab.org Message-ID: <835492.28231.qm(a)web51612.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE --------------------------------- Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.

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