- modeller_usage - salilab.org

Incorporation of hetero atom
by 서주현 13 Nov '06

13 Nov '06

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Re: [modeller_usage] How to use model.patch_ss_templates() ?
by Modeller Caretaker 08 Nov '06

08 Nov '06

jitrayut jitonnom wrote: > I am new for this program and i doubt on how to use > model.patch_ss_templates() in order to model disulfide bond of our model > from templates. As i read the FAQ no. 3, i am stil not understand that > where *_patch_disulfides.py_* be used. Since I know from the advanced > tutorials that there are many steps to run multiple template such as > salign.py , align2d_mult.py, model_mult.py, and evaluate_model.py. So, > which steps should be insertedt the patch_disulfides.py ? salign.py and align2d_mult.py are for alignment, and evaluate_model.py is for model evaluation. In all of these cases the definition of disulfide bonds is not required. model.patch_ss_templates() adds disulfide bonds in the model, if it is aligned with a template which has a disulfide. This is called automatically for you for 'automodel' so you don't generally need to worry about it. An example is given in FAQ #3 of how to add specific disulfide bonds in the 'automodel' procedure, using model.patch(). This only applies to the model building step, of course - model_mult.py in your case. 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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Hole in models
by hori koshii 02 Nov '06

02 Nov '06

Hi everybody. I am wondering if anyone has got holes in many of the homology models generated? Any ways to control this? Thanks for answering. Good day. Sincerely, --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster.

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errors after running the program
by gadde suneetha 29 Oct '06

29 Oct '06

Hello sir, I have executed the following code. 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='TvLDH.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') the following messages are displayed. 1)file build_profile.py line 6 in? seq_database_format='PIR', chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True) 2) file c:\programfiles\modeller8v2\modlib\modeller\util\top.py line 29 in read. libs=libs.modpt , **vars 3)file c:\programfiles\modeller8v2\modlib\modeller\util\top.py line 353 line in read_sequence_db return modeller.read_sequence_db(sdb,libs,*args) 4) IO error openf 670E)cannot open file pdb_95.PIR no such file or directory 1,2,3----are these errors or warnings. please kindly let me know the changes i have to make. Regards suneetha. __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/

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problem i running scrit program
by gadde suneetha 28 Oct '06

28 Oct '06

Hello frends I am a tyro in modeller. In modeller window version i have run a file x.py as mod8v2 x.py .the content in the file is from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', sequence = '1fdx') a.starting_model= 1 a.ending_model = 1 a.make() the error message is 'import site' failed; use -v for trace back. plz let me know what changes i have to do to overcome this error. regards suneetha __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/

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Picking Models
by hori koshii 26 Oct '06

26 Oct '06

Hi all. I am some doubts over picking model. Thank you for your time. Since I have to model two 12 aa loop regions, many loopmodels have to be generated (500 or 1000 as recommanded by others). I did a set of 100 and a set of 500. I used the DOPE score to compare them and the difference between the models with the minimum and maximum scores were around 1000 in both cases. So I just wonder, are you all using the lowest DOPE score to pick the best model? If so, will generated a set of 100 loopmodels be enough instead of 500 or a 1000? I shall also use the model for MD, so in this case, do I need to build so many loopmodels? Will MD suffice to explore the conformations? I am sorry for not understanding the concept of generating many loopmodels. Is the for "correctness" or exploring all the conformations? Thank you for reading this and sorry if my questions sound too inexperience. I am still learning and thank you very much for any help. (Also, I looked at profiles but sometimes the second best model seems to have better profile at the loop regions than the one with the lowest score, any other ways tthat you use to pick model?) --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail.

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What structure is better ??
by cristian obiol 26 Oct '06

26 Oct '06

Dear Modeller users, I have constructed a homology model of my human protein starting with a template of the yeast variant. The first problem I faced is that both proteins are very different, with only 23% homology. To solve possible errors in the best modeller structure I also carried out a 6ns molecular dynamics asuming that minor changes would happen. But I'm not sure if the first structure is the best one. And the option to performing a molecular dynamics for each modeller structure is very time consuming, moreover the RMS backbone deviation for the first five or ten ones is very small (0.8 to 1.1 A). Here it's my question : What is the normal protocol in order to obtain a good enough final structure ? Can I assume that choosing the following structures and performing a molecular dynamics simulation I will get almost the same final stuctures ? Thanks in advance for any suggestion. Cristian Obiol Biological Systems Modelling and Drug Design Research Group University of Barcelona

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max_molpdf and all hydrogen models
by Mike White 24 Oct '06

24 Oct '06

Hello, I believe that one reason that one cannot compare molpdf scores between models of different proteins is that it depends on the number of atoms in the protein- more atoms means a higher molpdf, even if it is a "good" model. Does this mean that if one is trying to do an all hydrogen model that the molpdfs will be much higher than that for the same protein modeled without hydrogens? The reason that I ask is that I am modeling a pentamer with an all hydrogen model, and each time the modeling stops after a few steps with the moldpdf stuck slightly higher than 100,000 (which is the default max_molpdf value) and then moves on to the next model, where this happens again (and again...). I assume that this is because of all of the additional hydrogens, and that if I just increase max_molpdf to 200,000 things should be fine. Is my underlying assumption correct? Thanks

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object classes-symmodel, automodel, allhmodel, etc.
by Mike White 24 Oct '06

24 Oct '06

Hi there, I have been building a set of models that have symmetry restraints in them, and I now want to build models with all hydrogens included. In the modelling script that I use, I create a symmodel object class symmodel(automodel) and then define the symmetry restraints followed by a=symmodel(env, alnfile='*', knowns=('*'), sequence='*') (the *'s represent the real file names used) and finally a.make() This works fine. However, looking over the script in the online manual for creating an all hydrogen model, one must use the allhmodel class a=allhmodel(...) . . a.make() in order to create the appropriate model. My question is, if I have already created a symmodel class to enforce symmetry restraints, how can I create an all hydrogen model, if that process requires an allhmodel class object? I am a novice with Python, my understanding of objects is at best rudimentary. Thanks for your help Mike White

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how to evaluate 100 profiles?
by hori koshii 20 Oct '06

20 Oct '06

Hi, does anyone know python and modeller very well and give us some help to run a model evaluation script for 100 homology models. (how to set 'EGPh.B99990001.pdb' as a variable and make it like a loop so the number can be increased by 1 in the next run), or another other ways you know? It will be so appreciated and thanks. The items need to be updated in the loop are bolded in the following script. ---------------------------------------------------------------------------------------------------------------------- from modeller import * 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' # read model file mdl = model(env) mdl.read(file='EGPh.B99990001.pdb') aln = alignment(env) code = "EGPh" # generate topology aln.append_model(mdl, atom_files='EGPh.B99990001.pdb', align_codes=code) aln.append_model(mdl, atom_files='EGPh.B99990001.pdb', align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='EGPh.profile', normalize_profile=True, smoothing_window=15) ---------------------------------------------------------------------------------------------------------------------------- EGPh.BL01220001.pdb EGPh.BL01570001.pdb EGPh.BL01920001.pdb EGPh.BL01230001.pdb EGPh.BL01580001.pdb EGPh.BL01930001.pdb EGPh.BL01240001.pdb EGPh.BL01590001.pdb EGPh.BL01940001.pdb EGPh.BL01250001.pdb EGPh.BL01600001.pdb EGPh.BL01950001.pdb EGPh.BL01260001.pdb EGPh.BL01610001.pdb EGPh.BL01960001.pdb EGPh.BL01270001.pdb EGPh.BL01620001.pdb EGPh.BL01970001.pdb EGPh.BL01280001.pdb EGPh.BL01630001.pdb EGPh.BL01980001.pdb EGPh.BL01290001.pdb EGPh.BL01640001.pdb EGPh.BL01990001.pdb EGPh.BL01300001.pdb EGPh.BL01650001.pdb EGPh.BL02000001.pdb EGPh.BL01310001.pdb EGPh.BL01660001.pdb EGPh.IL00000001.pdb EGPh.BL01320001.pdb EGPh.BL01670001.pdb EGPh.BL01330001.pdb EGPh.BL01680001.pdb --------------------------------- Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.

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