- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 30
by salam pradeep 22 May '08

22 May '08

How do I installed Pylab for plotting the plot_profiles.py On Thu, May 22, 2008 at 10:00 PM, <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. EM density maps for building models? (Juan Chang) > 2. Re: EM density maps for building models? (Modeller Caretaker) > 3. Modeller 9v4 release (Modeller Caretaker) > 4. multiple template model (deepti nayar) > 5. Re: multiple template model (Modeller Caretaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 13 May 2008 12:49:35 -0400 > From: Juan Chang <juan.chang(a)bcm.edu> > Subject: [modeller_usage] EM density maps for building models? > To: modeller_usage(a)salilab.org > Message-ID: <4829C69F.6000108(a)bcm.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello, > > The density.grid_search() function outputs a 'bestCC_targ' file which > contains the CCF. Is there a way to use this information for model > building? A web tutorial or Python code on how to use electron > microscope density maps for model building would be helpful. > > Thanks! > > > ------------------------------ > > Message: 2 > Date: Tue, 13 May 2008 12:28:44 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] EM density maps for building models? > To: Juan Chang <juan.chang(a)bcm.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <4829EBEC.2030603(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Juan Chang wrote: > > The density.grid_search() function outputs a 'bestCC_targ' file which > > contains the CCF. Is there a way to use this information for model > > building? A web tutorial or Python code on how to use electron > > microscope density maps for model building would be helpful. > > grid_search is for static fitting of models into density maps, e.g. for > model assessment. It is not suitable for guiding the model building > procedure itself. You could, however, check out Flex-EM at > http://salilab.org/Flex-EM/ and check out the referenced paper to see if > that is helpful for you. > > 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, 15 May 2008 09:17:30 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: [modeller_usage] Modeller 9v4 release > To: modeller_announce(a)salilab.org, modeller_usage(a)salilab.org > Message-ID: <482C621A.5030005(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The new version of Modeller, 9v4, is now available for download! Please > see the download page at http://salilab.org/modeller/ for more > information. > > If you have a license key for Modeller 8 or 9, there is no need to > reregister for Modeller 9v4 - the same license key will work. (It won't > do any harm to reregister if you want to, though!) > > 9v4 is primarily a bugfix release relative to the last public release > (9v3). Major user-visible changes include: > > # The speed of GB/SA calculations has been dramatically increased. > # io_data.atom_files_directory is now a Python list of directories, > rather than a colon-separated string. (This is so that everything > works on Windows, where ':' is a valid character in directory names.) > Old scripts that use colon-separated strings should still work, but > will trigger a warning. > # When reading or writing compressed files, the uncompressed versions of > these files are now written into writeable local storage. Previously, > these files were written into the same directory as the compressed > versions, which is problematic when that directory is read-only or is > on network storage. > # Update PDB files used in the examples (remediated PDBs are now used). > > See the Modeller manual for a full change log: > http://salilab.org/modeller/9v4/manual/node38.html > > If you encounter bugs in Modeller 9v4, please see > http://salilab.org/modeller/9v3/manual/node10.html for information on > how to report them. > > 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: 4 > Date: Thu, 22 May 2008 12:24:33 +0530 > From: "deepti nayar" <deeptinayar(a)gmail.com> > Subject: [modeller_usage] multiple template model > To: modeller_usage(a)salilab.org > Message-ID: > <630ea2870805212354k4c5b5e5bmcb4cde2b08be5ca5(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all > > I am new to modeller. I am using modeller 9v2. I am trying to model > structure for a protein using two templates. Can anyone tell me > whethermodeller first builds its own alignment among the templates and then > build a model??? > > Is there a way by which we can get the model based on our wished alignment. > I tried this but it seems it doesnt work. > > thanks > > -- > Regards > > Deepti Nayar > Research Assistant > Bioinformatics Centre > National Institute of Immunology > New Delhi - 110067 > e-mail: deeptinayar(a)gmail.com >

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multiple template model
by deepti nayar 22 May '08

22 May '08

Hi all I am new to modeller. I am using modeller 9v2. I am trying to model structure for a protein using two templates. Can anyone tell me whethermodeller first builds its own alignment among the templates and then build a model??? Is there a way by which we can get the model based on our wished alignment. I tried this but it seems it doesnt work. thanks -- Regards Deepti Nayar Research Assistant Bioinformatics Centre National Institute of Immunology New Delhi - 110067 e-mail: deeptinayar(a)gmail.com

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Modeller 9v4 release
by Modeller Caretaker 15 May '08

15 May '08

The new version of Modeller, 9v4, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v4 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v4 is primarily a bugfix release relative to the last public release (9v3). Major user-visible changes include: # The speed of GB/SA calculations has been dramatically increased. # io_data.atom_files_directory is now a Python list of directories, rather than a colon-separated string. (This is so that everything works on Windows, where ':' is a valid character in directory names.) Old scripts that use colon-separated strings should still work, but will trigger a warning. # When reading or writing compressed files, the uncompressed versions of these files are now written into writeable local storage. Previously, these files were written into the same directory as the compressed versions, which is problematic when that directory is read-only or is on network storage. # Update PDB files used in the examples (remediated PDBs are now used). See the Modeller manual for a full change log: http://salilab.org/modeller/9v4/manual/node38.html If you encounter bugs in Modeller 9v4, please see http://salilab.org/modeller/9v3/manual/node10.html for information on how to report them. 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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EM density maps for building models?
by Juan Chang 13 May '08

13 May '08

Hello, The density.grid_search() function outputs a 'bestCC_targ' file which contains the CCF. Is there a way to use this information for model building? A web tutorial or Python code on how to use electron microscope density maps for model building would be helpful. Thanks!

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one question,please answer
by Maryam Nikoosaleh 12 May '08

12 May '08

Dear all, Hi! I have one question about evaluation of my built model by DOPE score. After building model, I refined the side chains of residues with SCWRL3 program.The total Dope score of initial model was better than the refined model;but the structure of two disallowed regions of my initial model (with DOPE score higher than -0.03) were become better. In evaluation of stereochemical features of built models by PROCHECK, the side chains , as we expected, became better . but the amount of bad contacts became more. Could you tell me please which model is better? (initial model or refined model) One note : Before refining by SCWRL3 ,I have refined the loops of my model with modeller;But it did not built a better model. Thanks for your attention. Best regards, Nikousaleh

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one question,please answer
by Maryam Nikoosaleh 12 May '08

12 May '08

Dear all, Hi! I have one question about evaluation of my built model by DOPE score. After building model, I refined the side chains of residues with SCWRL3 program.The total Dope score of initial model was better than the refined model;but the structure of two disallowed regions of my initial model (with DOPE score higher than -0.03) were become better. In evaluation of stereochemical features of built models by PROCHECK, the side chains , as we expected, became better . but the amount of bad contacts became more. Could you tell me please which model is better? (initial model or refined model) One note : Before refining by SCWRL3 ,I have refined the loops of my model with modeller;But it did not built a better model. Thanks for your attention. Best regards, Nikousaleh

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help at second script
by matziast＠med.uth.gr 08 May '08

08 May '08

Hi, While I was running the second script which is called compare.py and is the following: from modeller import * env = environ() aln = alignment(env) for (pdb, chain) in (('1b8p', 'A'), ('1bdm', 'A'), ('1civ', 'A'), ('5mdh', 'A'), ('7mdh', 'A'), ('1smk', 'A')): m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. suse:/home/maria # mod9v3 compare.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 7, in ? m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 23, in __init__ self.read(**vars) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 68, in read model_format, model_segment) IOError: pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz. .bz2) Please, help me.

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Loop Models
by Gilles Truan 07 May '08

07 May '08

Hi all, I created 5 models with a modified automodel script: a = automodel(env, alnfile = "bcs1h.fasta", knowns = ("1E32m", "1IXZm", "1IY1m", "1LV7m", "1S3Sm", "2CE7m", "2QZ4m"), sequence = ("bcs1h"), assess_methods=(assess.DOPE)) a.starting_model = 1 a.ending_model = 5 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level= refine.slow a.repeat_optimization = 2 a.max_molpdf = 1e6 a.make() These models have their OBJECTIVE FUNCTION around 11,000 . I made some DOPE plots to check for poorly defined regions. I detected some loops where the DOPE score was higher. I decided to further modelize these loops with loop_model as shown in the tutorial selecting residues having DOPE score significatively higher than the average DOPE for the entire structure. Here is the script: class MyLoop(loopmodel): def select_loop_atoms(self): return selection( self.residue_range(1, 26), self.residue_range(75,84), self.residue_range(89,97), self.residue_range(102,122), self.residue_range(183,204), self.residue_range(230,238)) for i in pdb_names: m = MyLoop (env, inimodel=("bcs1h.B9999000%s.pdb" %(i)), sequence=("bcsh1.%s" %(i)), library_schedule = autosched.slow, loop_assess_methods=(assess.DOPE, assess.GA341)) m.loop.starting_model= 1 m.loop.ending_model = 5 m.loop.md_level = refine.slow_large m.loop.max_var_iterations = 300 m.loop.library_schedule = autosched.slow m.make() Quite surprisingly, the OBJECTIVE function of the 25 produced loop models varies from 2000 to 7000 and the DOPE plots of the different loop models is not as good as the first models!! Is there something wrong in the script or do I need to change and optimize some other parameters? -------------------------------------------------------------- Dr. Gilles Truan Centre de Génétique Moléculaire, CNRS 1 Av. de la Terrasse, 91198 Gif-sur-Yvette, France Phone: 33-1-69 82 36 65, Fax: 33-1-69 82 36 82, <http://www.cgm.cnrs-gif.fr/pompon/index.html> Lab Web Site <mailto:gtruan@cgm.cnrs-gif.fr> Email --------------------------------------------------------------

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Error when using dope_loopmodel
by Florian Odronitz 07 May '08

07 May '08

Hi, i generated a model using the model_single.py example. So this is without loop modeling. Now I would like to model loops only, using the example from the manual: from modeller import * from modeller.automodel import * class my_lm(dope_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('535', '562')) env = environ() a = my_lm(env, alnfile='HsMhc1_best_no_loops_motor.ali', knowns='1DFK_motor', sequence='HsMhc1') a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 5 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() Please note that I used the dope_loopmodel class instead of loopmodel as indicated in the manual. When I run the script, it exits with the following message: report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 68 111 445 496 671 602 791 874 924 1041 << end of ENERGY. iatmcls_286W> MODEL atom not classified: GLU:OXT GLU preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Using dopehr_loopmodel gives the same error whereas the "old" loopmodel works. Here is the Atom record from the PDB file: ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 The coordinates do not seem to be out of range. I also put a blank in the middle ("1.00 103.06") to avoid problems with the parser, but to no avail. Am I doing something wrong here or is this a bug? Any help on this is greatly appreciated. Florian

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help at first script
by matziast＠med.uth.gr 05 May '08

05 May '08

Hi, I am a new user of modeller9v3 and I can't write the first script with which I will search for sequences similar to the target one. I also consult the manual of modeller6v2, will I confuse? If I have understood well, the appropriate command is sequence_search which has many options. I must use all the options? I can't understand the syntax of the command, i.e I must type mod9v3 before the command, but I read that the syntax is mod9v3 script_ .top. This script what does it contain? (I can't understand anything becose I start now to deal with bioinformatics). Please help me. Thank you very much, Maria.

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