modeller_usage December 2012

modeller_usage@salilab.org

10 participants
18 discussions

Fwd: modeling with multiple sequence alignment.
by Krupal Jethava 10 Dec '12

10 Dec '12

---------- Forwarded message ---------- From: Krupal Jethava <krupal.jethava(a)gmail.com> Date: Mon, Dec 10, 2012 at 5:12 PM Subject: Re: [modeller_usage] modeling with multiple sequence alignment. To: Rienk Doetjes <rienk(a)stereodax.com> I have these files. 1) *alignment2.ali* file for alignment between target (qseq) and templates (tseq1, tseq2). 2)* pdb* files of templates 2) *script.py* *I tried this script as first step.* 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='pdb_95.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='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL') #-- Now, read in the binary database sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL') #-- Read in the target sequence/alignment aln = alignment(env) aln.append(file='*alignment2.ali*', alignment_format='PIR', align_codes='ALL') #-- 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') *There is error* *cannot open logfile script.log: permission denied.* On Mon, Dec 10, 2012 at 5:04 PM, Rienk Doetjes <rienk(a)stereodax.com> wrote: > Could you provide more information? Could you post your script, the error > you receive, etc? > > On 10 Dec 2012, at 11:26, Krupal Jethava wrote: > > > Dear Sir, > > I am trying to use modeller for multiple sequence alignment but I got > error while running script for DOPE score. will you guide from the > beginning. how to make input file and which script should I use for that. > Thanks. > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > >

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Fwd: modeling with multiple sequence alignment.
by Krupal Jethava 10 Dec '12

10 Dec '12

---------- Forwarded message ---------- From: Krupal Jethava <krupal.jethava(a)gmail.com> Date: Mon, Dec 10, 2012 at 6:01 PM Subject: Re: [modeller_usage] modeling with multiple sequence alignment. To: flavio seixas <oivalf_nix(a)yahoo.com> *I have* *1) alignment.ali* *2) qseq.fasta* *2) tseq1.pdb and tseq2.pdb* * * *I tried this script by modeller- "C:\ program files (x86)\ modeller 9.11\ bin \ test> mod9.11 script.py"* # Homology modeling with multiple templates 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 = ['.', '../atom_files'] a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('tseq2', 'tseq1'), # codes of the templates sequence = 'qseq') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling *Got these errors* *traceback <.......>:* * file "script.py", line 18,in ?* *a.make()* *File ; C:\........\automodel.py, line 424 in homcsr,* *File ; C:\........\**automodel.py, line 406, in check_alignment* * aln.check()* and many....... What to do? On Mon, Dec 10, 2012 at 5:22 PM, flavio seixas <oivalf_nix(a)yahoo.com> wrote: > Hi, > > For multiple templates try to follow this example: > > http://salilab.org/modeller/9.10/manual/node21.html > > Try to put those lines below, at the end of your script model-multiple.py > script. > It will display the top five models at the end of your model-multiple.log > file. > > > # Get a list of all successfully built models from a.outputs > ok_models = filter(lambda x: x['failure'] is None, a.outputs) > > # Rank the models by DOPE score > key = 'DOPE score' > ok_models.sort(lambda a,b: cmp(a[key], b[key])) > > # Get top model > m = ok_models[0] > > print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) > m = ok_models[1] > > print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) > m = ok_models[2] > > print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) > m = ok_models[3] > > print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) > m = > ok_models[4] > > print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) > > > > Regards, > > Flavio > > > > > --- On Mon, 12/10/12, Krupal Jethava <krupal.jethava(a)gmail.com> wrote: > > From: Krupal Jethava <krupal.jethava(a)gmail.com> > Subject: [modeller_usage] modeling with multiple sequence alignment. > To: modeller_usage(a)salilab.org > Date: Monday, December 10, 2012, 11:26 AM > > Dear Sir, I am trying to use modeller for multiple sequence alignment > but I got error while running script for DOPE score. will you guide from > the beginning. how to make input file and which script should I use for > that. Thanks. > > -----Inline Attachment Follows----- > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >

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Re: [modeller_usage] modeling with multiple sequence alignment.
by flavio seixas 10 Dec '12

10 Dec '12

Hi, For multiple templates try to follow this example: http://salilab.org/modeller/9.10/manual/node21.html Try to put those lines below, at the end of your script model-multiple.py script. It will display the top five models at the end of your model-multiple.log file. # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) Regards, Flavio --- On Mon, 12/10/12, Krupal Jethava <krupal.jethava(a)gmail.com> wrote: From: Krupal Jethava <krupal.jethava(a)gmail.com> Subject: [modeller_usage] modeling with multiple sequence alignment. To: modeller_usage(a)salilab.org Date: Monday, December 10, 2012, 11:26 AM Dear Sir, I am trying to use modeller for multiple sequence alignment but I got error while running script for DOPE score. will you guide from the beginning. how to make input file and which script should I use for that. Thanks. -----Inline Attachment Follows----- _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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modeling with multiple sequence alignment.
by Krupal Jethava 10 Dec '12

10 Dec '12

Dear Sir, I am trying to use modeller for multiple sequence alignment but I got error while running script for DOPE score. will you guide from the beginning. how to make input file and which script should I use for that. Thanks.

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Re: [modeller_usage] Fwd: Modelling of Chimeric protein
by flavio seixas 09 Dec '12

09 Dec '12

Hi James. Maybe if you post your script, it becomes more easier to help. But, from your post I can see that the lenght of your target and sequence alignment are not equal. See from http://salilab.org/modeller/9.10/manual/node21.html that the differences in the lenght are filled with "-" Maybe you should check this. Regards, Flavio --- On Sun, 12/9/12, James Starlight <jmsstarlight(a)gmail.com> wrote: > From: James Starlight <jmsstarlight(a)gmail.com> > Subject: Re: [modeller_usage] Fwd: Modelling of Chimeric protein > To: "flavio seixas" <oivalf_nix(a)yahoo.com> > Date: Sunday, December 9, 2012, 6:23 PM > Hi Flavio! > > In the align-multiple.ali file > structureN:3u10:470 ::203 : :::-1.00:-1.00 > 470 is the number of first residue (in pdb file) and 203 is > the length > of the sequence of that protein > > I have superimpose both of the templates and locate them in > the > desired location in the initial pdb's templates. > > > Is there any string that I should add to my script ? > ( that example I have used http://salilab.org/modeller/9.10/manual/node21.html ) > > Also I've added the string automodel.initial_malign3d= True > but there were no difference in the output modell > > James > > 2012/12/9, flavio seixas <oivalf_nix(a)yahoo.com>: > > Hi James, > > > > I have 2 suggestions. > > > > 1) The alignment file of your second template is set: > >> >P1;3u10 > >> structureN:3u10:470 ::203 : :::-1.00:-1.00 > > > > I think the correct must be (first residie to last > residue): > >> >P1;3u10 > >> structureN:3u10:203 ::470 : :::-1.00:-1.00 > > > > > > 2) Did you put both templates in the same coordinated > system? I mean, did > > you superpose (Secondary Strucuture Match supermpose) > both the templates in > > a way that generated models will reflect the template > structure? > > > > Regards > > > > Flavio > > > > --- On Sun, 12/9/12, James Starlight <jmsstarlight(a)gmail.com> > wrote: > > > >> From: James Starlight <jmsstarlight(a)gmail.com> > >> Subject: [modeller_usage] Fwd: Modelling of > Chimeric protein > >> To: "modeller_usage" <modeller_usage(a)salilab.org>, > "Modeller Caretaker" > >> <modeller-care(a)salilab.org> > >> Date: Sunday, December 9, 2012, 11:25 AM > >> Dear Modeler Users! > >> > >> > >> Recently I've done my chimeric protein based on > two > >> different > >> templates in accordance to the > >> http://salilab.org/modeller/9.10/FAQ.html#1 > >> > >> using that script > >> http://salilab.org/modeller/9.10/manual/node21.html > >> > >> below the alignment of my templates as well as > sequence > >> > >> >P1;1gfl > >> structureX:1gfl:1 ::238 : :::-1.00:-1.00 > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* > >> > >> >P1;3u10 > >> structureN:3u10:470 ::203 : :::-1.00:-1.00 > >> > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL.* > >> > >> >P1;seq > >> sequence:seq: : : > >> : ::: 0.00: 0.00 > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH* > >> > >> > >> As the result I've obtain model where first > template ( > >> beta-can GFP) > >> was in correct form but the conformation of the > second > >> protein was > >> differ from the used template ( pdb id 3u10). > >> > >> > >> Could you tell me why my model was so distorted and > how I > >> can improve > >> it further? > >> > >> Thanks for help > >> > >> James > >> > >> 2012/8/8, Modeller Caretaker <modeller-care(a)salilab.org>: > >> > On 8/8/12 6:27 AM, James Starlight wrote: > >> >> I want to model chimeric protein which > consist of > >> two fussed proteins > >> >> ( tail to head fussion C to N termi). > It's > >> important that both of that > >> >> proteins have known spatial structures > which could > >> be used as the > >> >> templates. > >> > > >> > http://salilab.org/modeller/9.10/FAQ.html#1 > >> > > >> >> Is there any way to use both of the > templates to > >> guide such modelling > >> >> ? In the input option I've found only > possibility > >> to use one template. > >> > > >> > 'knowns' can be a list of multiple templates. > See > >> > http://salilab.org/modeller/9.10/manual/node21.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 > >> > > >> > >> _______________________________________________ > >> modeller_usage mailing list > >> modeller_usage(a)salilab.org > >> https://salilab.org/mailman/listinfo/modeller_usage > >> > > >

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Fwd: Modelling of Chimeric protein
by James Starlight 09 Dec '12

09 Dec '12

Dear Modeler Users! Recently I've done my chimeric protein based on two different templates in accordance to the http://salilab.org/modeller/9.10/FAQ.html#1 using that script http://salilab.org/modeller/9.10/manual/node21.html below the alignment of my templates as well as sequence >P1;1gfl structureX:1gfl:1 ::238 : :::-1.00:-1.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* >P1;3u10 structureN:3u10:470 ::203 : :::-1.00:-1.00 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL.* >P1;seq sequence:seq: : : : ::: 0.00: 0.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH* As the result I've obtain model where first template ( beta-can GFP) was in correct form but the conformation of the second protein was differ from the used template ( pdb id 3u10). Could you tell me why my model was so distorted and how I can improve it further? Thanks for help James 2012/8/8, Modeller Caretaker <modeller-care(a)salilab.org>: > On 8/8/12 6:27 AM, James Starlight wrote: >> I want to model chimeric protein which consist of two fussed proteins >> ( tail to head fussion C to N termi). It's important that both of that >> proteins have known spatial structures which could be used as the >> templates. > > http://salilab.org/modeller/9.10/FAQ.html#1 > >> Is there any way to use both of the templates to guide such modelling >> ? In the input option I've found only possibility to use one template. > > 'knowns' can be a list of multiple templates. See > http://salilab.org/modeller/9.10/manual/node21.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 >

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results analysis
by sdimicco 07 Dec '12

07 Dec '12

Dear Modellers, I am building a multimeric protein. The DOPE and GA341 scores are developed for single chain models. How can I asses the quality of my models? The sole molpdf is sufficient? Moreover, as I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it? Thank you in advance All the best Simone

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loop refinement
by Urszula Uciechowska 01 Dec '12

01 Dec '12

Dear Modeller users, I was trying to use the script for the loop refinement, however I want to use several templates codes. I tried to add them as: knowns = '5fd1', '1tre', '1j8h' , # codes of the templates and received an error: File "loop_model.py", line 13 knowns = '1tcrA','3mbeC','2q86A','3c6lA','1j8hD', #templates SyntaxError: non-keyword arg after keyword arg How should I specify them? # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 4 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling thanks a lot for your help /Urszula

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modeller_usage December 2012