modeller_usage December 2005

modeller_usage@salilab.org

19 participants
24 discussions

out_put directory
by doppelt olivia 28 Dec '05

28 Dec '05

Hello, I have a problem concerning the output_directory in modeller. I changed it on my script but the thing is that it generates errors because the restraint file and the .ini file is not found by the automodel script. Is there a way to only put the models in a file?? instead of modifying the entire output_directory?? Please, help me Olivia --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta.

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what i am doing wrong?
by Anna Kaczynska 24 Dec '05

24 Dec '05

Dear all, I am just starting with Modeller and I am trying to run the 'basic-example' that is posted on-line, but it does not work. Can you let me know what I am doing wrong? Thank you sincerely Anna Kaczynska Type 'mod8v1 model-default.py' to run Modeller on the script 'model- default.py'. C:\Program Files\Modeller8v1>mod8v1 model-default.py FATAL ERROR: Cannot open file model-default.py: No such file or directory C:\Program Files\Modeller8v1>basic example dir 'basic' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1>c: C:\Program Files\Modeller8v1>cd basic-example C:\Program Files\Modeller8v1\basic-example>dir Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,568,976,896 bytes free C:\Program Files\Modeller8v1\basic-example>dir Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,568,976,896 bytes free C:\Program Files\Modeller8v1\basic-example>P1;TvLDH 'P1' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1\basic-example>DIR Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,569,390,592 bytes free C:\Program Files\Modeller8v1\basic-example>P1;TvLDH 'P1' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1\basic-example>

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modelling loops with nmr restraints
by cubellis＠unina.it 16 Dec '05

16 Dec '05

dear sir , I am trying to model a protein using an alignment to a pdb template and nmr data for a loop which is missing in the pdb template. the input top file that used is the following: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ATOM_FILES_DIRECTORY = './' SET PDB_EXT = '.pdb' #SET MD_LEVEL = 'refine1' SET HYDROGEN_IO = on #SET DEVIATION = 4.0 SET ALIGNMENT_FORMAT = 'PIR' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET SEQUENCE = 'mysequence' SET ALNFILE = 'my.ali' SET KNOWNS='mytemplatestructure' SET TOPOLOGY_MODEL = 1 SET TOPLIB = '/software/modeller7v7/modlib/top_allh.lib' SET PARLIB = '/software/modeller7v7/modlib/par.lib' CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE I obtained 10 models but I can see that none of them satisfies all the nmr restraints. therefore I thought to model more thoroughly only the loop for which I have the nmr restraints. could you suggest me how to include in the proper way when I call the loop routine? shall I use again SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE ? or shoud I read only the nmr.rsr? or other options? -many thanks mvcubellis ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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DOPE Score
by Mattias de Hollander 16 Dec '05

16 Dec '05

Hi, I've a question about the DOPE score and the profile plot you can make of it using GNUPLOT. I made such a plot with the files from the basic tutorial. When i do the same for my own data, i don't get a nice plot. I made the profiles using the script of the tutorial and the pdb files of my model and template. The data range of the dope score for each residue is different for my model and the template. So you see the line of the template with the line of the model far below it in a straight line (due to the differences in data range) The final DOPE scores are also different. Does this mean i have a wrong model? The model i use is the best of 20 generated models and i did check it with procheck and errat. The last one even gives a good score (84) and doesn't shows any black areas. So, what's wrong? Does the dope score not work on my files? Thanks, Mattias -- Student Bio-Informatics Hogeschool Leiden The Netherlands

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Loop model selection
by bmbbl＠leeds.ac.uk 15 Dec '05

15 Dec '05

Dear Modellers, I have used MODELLER to create 100 11-residue long loop models. Some of models cannot form proper loops, so I used their objective function value as cut-off to select loop models. However further biological structure-function studies of the selected models are not all consistent with the experiment results in vitro. Presumbaly, therefore, some of loop models shouldnot have been selected. Meanwhile I threw the crystal structure of the template into MODELLER to model the loop region, which is the corresponding position in the target model. The loop redefinement of the crystal structure show very similar conformations distribution to the model protein. In the crystal structure, 3 H-bonds stabilise the loop conformation. They are E-R , E-S. However R and S are replaced by P and T in the model sequence. So my questions is what the proper criteria is for this case? Should the conservation of the H-bonds be checked in the loop models? If it is a way how to check H-bonds in 100 loop models automatically before I have some ideas to write a piece of program myself? Many thanks for hints. Binbin

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is LOOP threading a common result?
by Starr Hazard 14 Dec '05

14 Dec '05

Folks, I am using Mod8v1 on a MAC G5 running OSX 10.3. In a protein with about 500 aa there was about a 100 amino acid region which did not match the single available template. I asked Modeller to make 1000 loops in the gap region. The happened and after a few fits I got the DOPE analysis of all 1000 loops complete. I picked the best 20 loops (lowest overall DOPE scores;minimal plots in the loop region) and examined these structures. In every one of the best twenty AND in the worst loop model, I see regions where the routines have threaded the loop though the nonloop regions of the original model. In words, suppose I have two antiparallel beta sheet strands. The backbone of the loop sometimes passes between these sheet stands or through the turn loop at the ends of the sheets before coursing away from the existing protein. Do the loop generator routines pay any attention at all to the nonloop regions? In older versions of Modeller, the routines would create knots where the insertions in the alignment were present. The alignment could be adjusted to prevent this. How can I persuade modeller not to thread regions of loop through "existing" non loop regions of the protein? Starr

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beta-sheets and alpha-helixes
by Matthias Negri 14 Dec '05

14 Dec '05

Hello, my name is Matthias and I'm a PhD Student at University of Saarland. I'm trying to model a cypP450 with modeller7v7 by defining the secondary structure (alpha, sheet..) in the special_restraints ROUTINE, but I still get error messages and the job is broken up! That's the error message I got: "Dynamically allocated memory at amaxseq [B,kB,MB]: 39334681 38412.773 37.512 TOP_________> 169 174 CALL ROUTINE = 'special_restraints' TOP_________> 170 479 SET ADD_RESTRAINTS = ON TOP_________> 171 480 MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '; 228:A' '253:A' assgn___215E> Dynamic memory allocation failed. Routine, variable, status: vars%val 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1" While my top file (special_restraints) is: "SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '228:A' '253:A' MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '140:A' '159:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '464:A' '467:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '480:A' '484:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '490:A' '495:A' RETURN END_SUBROUTINE" 1.Can you tell me what the reason for failing is? 2.Further, does modeller8.1 resolve this problem (if there is a bug in mod7v7?)! 3.I even get the error disclaimer: "openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 196 233 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL CYP17.sch TOP_________> 197 234 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 198 235 CALL ROUTINE = 'single_model_pass' TOP_________> 199 253 READ_MODEL FILE = MODEL,MODEL_SEGMENT = '31:A' '496:A' openf5__224_> Open 11 OLD SEQUENTIAL Mixed1.ini openf5__224_> Open 11 OLD SEQUENTIAL Mixed1.ini rdatm___297_> Segments, residues, atoms: 1 466 7457 rdatm___298_> Segment: 1 31 A 496 A 7457 TOP_________> 200 254 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 201 255 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 202 256 PICK_RESTRAINTS ADD_RESTRAINTS = OFF nselat__596E> Atom index is out of range (iatm,natm): 7458 7457 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 39111561 " What's the reason for, where I do mistakes? Thanks in advance, Matthias Negri 8.2 Pharmaceutical and Medicinal Chemistry Saarland University P.O.Box 151150 66041 Saarbrücken, Germany phone: +49-681-302-2980 fax: +49-681-302-4386 Email: m.negri(a)mx.uni-saarland.de http://www.uni-saarland.de/fak8/hartmann Computational Medicinal Chemistry Group Dept. of Pharmaceutical Sciences, University of Bologna Via Belmeloro, 6; 40100 Bologna, Italy Email: thias(a)scfarm.unibo.it http://www.scfarm.unibo.it

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(no subject)
by mahboobeh zarrabi 14 Dec '05

14 Dec '05

hi how can i model protein consist of heteroatoms(K ion and water)? thanks

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Re: modeller_usage Digest, Vol 4, Issue 113
by rathankar rao 09 Dec '05

09 Dec '05

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 http://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. file name problem (Starr Hazard) 2. Re: file name problem (Modeller Caretaker) 3. Re: To Model missing domains in the content of the rest (Shirley Li) 4. To use separate templates for different region of a protein (Shirley Li) ---------------------------------------------------------------------- Message: 1 Date: Thu, 08 Dec 2005 13:53:38 -0500 From: Starr Hazard Subject: [modeller_usage] file name problem To: modeller_usage(a)salilab.org Message-ID: Content-Type: text/plain; charset=us-ascii; format=flowed Folks, The following lines: mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file=code+'.profile', normalize_profile=True, smoothing_window=15) are producing output files with a question mark in the name string. ABC31_HUMAN.BL09950001.pdb?.profile The question mark renders cp, mv and rename incapable of doing anything with the file. Is there a way to prevent modeller from appending the question mark to the created files? Thanks, Starr ------------------------------ Message: 2 Date: Thu, 08 Dec 2005 11:17:16 -0800 From: Modeller Caretaker Subject: Re: [modeller_usage] file name problem To: Starr Hazard Cc: modeller_usage(a)salilab.org Message-ID: <439886BC.6050700(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Starr Hazard wrote: > mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', > file=code+'.profile', > normalize_profile=True, smoothing_window=15) > > are producing output files with a question mark in the name string. > > ABC31_HUMAN.BL09950001.pdb?.profile If this is from your earlier script, you're getting 'code' from the following bit of Python: code = in_file.readline() Note that readline() does not remove the line-end character(s), and that's probably confusing Modeller. Try putting in code = code.rstrip('\r\n') after you read the line from your file. > The question mark renders cp, mv and rename incapable of doing anything > with the file. You can just quote the filename, or escape the ? with a \ character, to make cp, mv and friends work with it. 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: Thu, 8 Dec 2005 13:15:23 -0800 (PST) From: Shirley Li Subject: [modeller_usage] Re: To Model missing domains in the content of the rest To: modeller_usage(a)salilab.org Message-ID: <20051208211523.94416.qmail(a)web53801.mail.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear MODELLER experts, I have a target protein, whose X-ray structure is PARTIALLY available (the middle part, named domain B). There are two big regions missing (domain A & C) in the crystal structure, with more than 50 residues in each I would like to use MODELLER to model domain A & C, and there are templates available. I wonder if it is possible to include THE CONTENT OF domain B. in another word, to create a complete model of A-B-C while keep the coordinates of B domain fixed. Any help/information will be greatly appreciated. hi its possible, just include the sequence of domain B in the ali file along with the seqence of domains A and B . the program will definitely orient the known structure with the calculated structure, but still u have to minimize it later on to infer the proper alignment with regards rathankar Shirley --------------------------------- __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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loops iterations and various DOPE scores
by Starr Hazard 09 Dec '05

09 Dec '05

Folks, I am having several difficulties with analysis of my loops. I built a model and selected a region to refine as a loop. I have successfully created 1000 loop files. Based on the model_energies.py file from the examples, I am attempting to scan the 1000 loop model files. So far the script manages to read only about 250 of the set. Here's the script. The file "loop.list" has the names of the 1000 files, one per line: ___________________________ 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 env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters # directories for input atom files env.io.atom_files_directory = './:../atom_files' def dope_profile(mdl, file): # DOPE energy parameters edat = energy_data(contact_shell=15.0, dynamic_modeller=True, dynamic_lennard=False, dynamic_sphere=False, excl_local=(False, False, False, False)) # DOPE group restraints oldgprsr = mdl.group_restraints if not model.dope_restraints: model.dope_restraints = \ group_restraints(classes='${LIB}/atmcls-mf.lib', parameters='${LIB}/dist-mf.lib') mdl.group_restraints = model.dope_restraints molpdf = mdl.energy(output='SHORT', file=file, edat=edat, residue_span_range=(1, 9999), normalize_profile=True, smoothing_window=10) mdl.group_restraints = oldgprsr return molpdf filename = 'loop.list' in_file = open(filename,"r") while 1: # read model file code = in_file.readline() mdl = model(env) mdl.read(file=code) aln = alignment(env) # generate topology aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code, align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) if info.version_info == (8,0): dope_profile(mdl, code+'.profile') else: mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file=code+'.profile', normalize_profile=True, smoothing_window=15) _____________________________________ Here are the first five lines of an output profile: __________________________________________________________ # Energy of each residue is written to: ABC31_HUMAN.BL00010001.pdb .profile # The profile IS normalized by the number of restraints. # The profiles are smoothed over a window of residues: 13 # The sum of all numbers in the file: -15.0456 ___________________________________________________ The actual profile file name looks like this "ABC31_HUMAN.BL00010001.pdb?.profile" 1a) So, Is there a limit to ability of Modeller or python to handle long file name strings? 1b) Why am I not able to digest all 1000 loop models? 2) In the log file that's produced I see a line like this for the first loop model: DOPE score :-51270.746094 What is the relationship between the summed per residue values from the profile output (ie -15.0456) and this DOPE score from the log file? Thanks, Starr

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modeller_usage December 2005