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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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scoring function and optimization
by sdimicco 26 Nov '12

26 Nov '12

Dear Modellers, I have three points to discuss. 1) As I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it? 2) 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? 3) I found thie messagge in the log file: Treating residue type GSH as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. I have understood that the input PDB file is the .ini, which is written during the calculation. Thus, how can I "remove the corresponding 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define it as my own residue? Thank you in advance All the best Simone

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(no subject)
by Shota Nakamura 20 Nov '12

20 Nov '12

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Error while running compare.py
by Anogna 20 Nov '12

20 Nov '12

Dear Modeller Users, I trying simple modelling methodology to model required protein structure. Till build_profile.py everything went well. But when gave compare.py.....i am get an error as follows *Traceback (most recent call last):* * File "compare.py", line 11, in ?* * m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) * * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 72, in __in* *it__* * self.read(**vars)* * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 117, in rea* *d* * model_format, model_segment)* *IOError: pdbnam_____E> Filename for PDB code not found: 3d3l* * Directories: .;atom_files* * Extensions : ;.atm;.pdb;.ent;.crd* * (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, * * and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)* Do I need make any modifications in my compare.py file....I am attaching compare.py file which i used. Please help me with this problem. Thanking You, Anogna

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optimization protocol and HETATM flexibility
by sdimicco 20 Nov '12

20 Nov '12

Dear Modellers, I am tring to set up my script to build a multimeric model with loop refinement. The script looks like: log.verbose() class dope_loopmodel(dope_loopmodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B'], renumber_residues=[1, 1]) env = environ() env.io.hetatm = True a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 2 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1e6 a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() automodel.final_malign3d = True It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that? Thank you in advance. Bests Simone

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Modeller Help
by mario rossi 19 Nov '12

19 Nov '12

Hello everyone I'am Simone an italian student, ineed to learn to use modeller to do homology modelingbut i have some trouble. I downloaded and installed both modeller and python on my pc (windows 7). To learn what to do I tried to follow the basic tutorial but I find serious problems in giving the input. I can not even load the sequence as the file (.ali) is not recognized by python and if the command is entered manually, I get syntax error?? Can you help me to understand where is the mistake?

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multimeric model and loop refinement
by sdimicco 16 Nov '12

16 Nov '12

Dear Member, I am trying to built a multimeric model. I would like to if I have to use restraints symmetry to model it. Moreover, i would like to built a model with all hydrogens and to refine loop automatically. How can I do that? I am trying to use allh model and loop model in the same script, but without success. Thank you in advance Simone

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