December 2012 - modeller_usage

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

12 Dec '12

Hi James. Thanks for the return. Have fun! Flavio --- On Wed, 12/12/12, 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: Wednesday, December 12, 2012, 1:58 PM > Thanks Flavio! It works perfect! > > James > > 2012/12/10, flavio seixas <oivalf_nix(a)yahoo.com>: > > Hi James! > > > > I am glad to help. > > > > The easier way to include hetatoms to model is to treat > them as BLK, with > > the single letter code "."(dot) > > > > In the alignment file, put "." at the position of your > hetatms, eg: > > > > aaaaaaaa---------.- (dot refers to > hetatm of the first template) > > --------bbbbbbbbb-. (dot refers to > hetatm of the second template) > > ccccccccccccccccc.. (model with hetatm > of both templates) > > > > To make your life easier, renumber the templates > sequentially. E.g., > > renumber the first template from 1 to 200 (hetatm is > 401) and the second > > from 201 to 400 (hetatm is 402). > > > > The hetatm of the first and second templates must be > renumbered as they will > > appear in the final model (as alignment above). > > > > Do not forget to put in your script file: > > > > # Read in HETATM records from template PDBs > > env.io.hetatm = True > > > > See http://salilab.org/modeller/manual/node18.html > for details. > > > > Regards, > > > > Flavio > > > > > > > > > > > > --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 6:33 PM > >> Hi, Flavio! > >> > >> Thanks for advises! I've used Nedit and exactly the > problem > >> was in the > >> incorrect alignment of y input data. With the > corrections > >> the modeler > >> produced very good models. > >> > >> Could you also tell me about possible options to > include > >> HETATM groups > >> from templates to the model? > >> > >> E.g both of my templates have two HETATM groups; > from GFP > >> protein its > >> chromophore group which is covalently bonded to > the > >> polypeptide chain > >> (like retinal in rhodopsin or HEM in globins) of > that > >> protein. > >> from the second globular domain- its small cyclic > GMP > >> molecule which > >> is the diffusive ligand of that protein. > >> > >> In the final model I'd like to include both of the > groups > >> from both of > >> the templates (chromophore to the GFP part as well > as cGMP > >> to the > >> interior of the second protein). > >> > >> By the way should I define chromophore group as the > part of > >> the first > >> (gfp) as well as 3rd (output fussed chimera) > sequence or > >> there is > >> another way to its inclusion ? > >> > >> Thanks for help again, > >> > >> James > >> > >> 2012/12/10, flavio seixas <oivalf_nix(a)yahoo.com>: > >> > Hi James, > >> > > >> > Modeller results are reproducible. I see you > are > >> producing just one model. > >> > Each time you run your script, it will produce > the same > >> model with the same > >> > error. > >> > > >> > Try to run more models and compare them. Try > at least > >> 100. I usually > >> > produces 1000 and select the best by modeller > dope > >> score and procheck > >> > evaluation. > >> > > >> > First of all, try to correct your alignment > file. > >> > > >> > Your alignment file still incorrect (see > attached). I > >> see that in your file, > >> > the sequences are: > >> > > >> > > >> > aaaaaa------* > >> > ----bbbbbbb* > >> > ccccccccccccccc* > >> > > >> > > >> > All sequences must have the same length! > >> > > >> > Maybe this is a problem with your text editor. > Try to > >> use Nedit (for linux). > >> > This editor does not have limits for number of > columns > >> and does not break > >> > the lines. > >> > > >> > I suggest you use Uniprot tab for alignment > >> (www.uniprot.org) > >> > > >> > You can display the alignment in fasta or pir > format. > >> > > >> > regards, > >> > > >> > Flavio > >> > > >> > > >> > > >> > > >> > --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 7:26 AM > >> >> Flavio, > >> >> > >> >> below you could find my script as well as > new > >> alignment > >> >> file. That > >> >> inpud data produces still wrong result in > the > >> conformation > >> >> of second > >> >> template > >> >> > >> >> # 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 = 'align-multiple.ali', # > alignment > >> filename > >> >> > >> >> knowns = ('1gfl', '3u10'), > >> >> # codes of the templates > >> >> sequence = > >> >> 'seq') > >> >> # code of the target > >> >> automodel.initial_malign3d= True > >> >> 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 > >> >> > >> >> > >> >> >P1;1gfl > >> >> structureX:1gfl:1 ::238 : > :::-1.00:-1.00 > >> >> > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* > >> >> > >> >> >P1;3u10 > >> >> structureN:3u10:470 :A:671 : > :A::-1.00:-1.00 > >> >> > >> > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASM > >> >> > >> > PLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASV > >> >> > RADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* > >> >> > >> >> >P1;seq > >> >> sequence:seq: : : > >> >> : ::: 0.00: 0.00 > >> >> > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH* > >> >> > >> >> > >> >> by the way do you know any web servers > for > >> produccing such > >> >> multiple > >> >> ali files for modeller input like > >> >> aaaa---- > >> >> ----bbbb > >> >> > >> >> for protein aaaabbbb > >> >> ? > >> >> > >> >> ( the above file I've done manually) > >> >> > >> >> James > >> >> > >> >> > >> >> 2012/12/9, flavio seixas <oivalf_nix(a)yahoo.com>: > >> >> > 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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modeller on windows 7
by Krupal Jethava 12 Dec '12

12 Dec '12

Hi, Please help me in this regard. I was working on windows XP with Modeller 9v5 and python v 2.5.1. Now I have another PC with Windows 7 Ultimate. I tried to run modeller 9v5 and python 2.5.1. on windows7. There was no error and no files generated in folder. What should I do? Is it because of wrong combination of modeller and python. If yes then which versions I should use. script I used. # 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 = ('tseq.pdb'), # 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 Thanks in advance.

2 1

(no subject)
by mario rossi 12 Dec '12

12 Dec '12

http://tummyfitindia.com/wp-content/plugins/google.html

1 0

Protein-ligand simulate annealing
by flavio seixas 11 Dec '12

11 Dec '12

Hi Ben I successfully generate charmm force fields (parameter and topology files) using swissparam server, for the ligand that is bonded to my protein template. Now I want to built models bonded to this ligand and also optimize them using Modeller protocol for MD and SA. My questions are: 1) How can I make modeller reads the parameter and topology files for the ligand? Is there a command for it? 2) Or should I copy and paste the ligand topology data to top_heav.lib file? 3) If the second option is the choice, where to paste the information regarding the parameters? 4) In the alignment file, how to set the symbol for the ligand? I think if I set it as BLK "." no changes will be made. Is that right? Best regards, Flavio

2 1

mutate protion dimer
by Sangita Kachhap 11 Dec '12

11 Dec '12

hello All I have a protein dimer and I have to insert amino acid rsidues in both monomer at same palce. Is it possible to do with Modller without affecting interaction between protein in crystal structure? With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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scoring function and optimization
by sdimicco 11 Dec '12

11 Dec '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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Regarding Salign Constructed Matrix
by Ashish Runthala 11 Dec '12

11 Dec '12

Dear Modellers, Whenever the SAlign is implemented with a set of templates, it generates a matrix showing some mutual similarity of templates (pairwise equivalences), something like this (against the target with 326 residues). 1SMQA 1H0OA 1SMQA 0 168 1H0OA 0 0 Now, answer me a set of queries. 1. Is 168 showing the count of similar residues, falling within the specified RMSD threshold? 2. Is this calculation considering LGA algorithm? 3. As there are certain folds existing in every such alignment, is there any lower limit of the existing residues in every such chunk to be considered similar. Like, if a fold is more than 3 residues long, i will take it similar in the matrix, and thus i would leave all the nuclear aligned residues. Is it considered this way in the program? Best, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 20, 2012 9:54:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 109 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. Re: Modeller Help (Modeller Caretaker) 2. optimization protocol and HETATM flexibility (sdimicco) 3. Error while running compare.py (Anogna) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Nov 2012 13:15:30 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> To: mario rossi <sanzodenzel(a)yahoo.it> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Modeller Help Message-ID: <50AAA172.6070202(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/19/2012 05:59 AM, mario rossi wrote: > 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? It's difficult to know what the problem is without a clearer description of what you did, and what results you got. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 20 Nov 2012 15:32:18 +0100 From: sdimicco <sdimicco(a)unisa.it> To: <modeller_usage(a)salilab.org> Subject: [modeller_usage] optimization protocol and HETATM flexibility Message-ID: <6dfdf81fe2a43f4c7bb0d6c96c07e6d5(a)unisa.it> Content-Type: text/plain; charset="utf-8" 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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Is the DOPE score good for evaluating transmembrane proteins model-structures?
by doranhen＠post.tau.ac.il 10 Dec '12

10 Dec '12

Hi, I was wondering whether I can use the DOPE score to evaluate models of transmembrane proteins? Thank you, Doran

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Re: [modeller_usage] Fwd: Modelling of Chimeric protein
by flavio seixas 10 Dec '12

10 Dec '12

Hi James! I am glad to help. The easier way to include hetatoms to model is to treat them as BLK, with the single letter code "."(dot) In the alignment file, put "." at the position of your hetatms, eg: aaaaaaaa---------.- (dot refers to hetatm of the first template) --------bbbbbbbbb-. (dot refers to hetatm of the second template) ccccccccccccccccc.. (model with hetatm of both templates) To make your life easier, renumber the templates sequentially. E.g., renumber the first template from 1 to 200 (hetatm is 401) and the second from 201 to 400 (hetatm is 402). The hetatm of the first and second templates must be renumbered as they will appear in the final model (as alignment above). Do not forget to put in your script file: # Read in HETATM records from template PDBs env.io.hetatm = True See http://salilab.org/modeller/manual/node18.html for details. Regards, Flavio --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 6:33 PM > Hi, Flavio! > > Thanks for advises! I've used Nedit and exactly the problem > was in the > incorrect alignment of y input data. With the corrections > the modeler > produced very good models. > > Could you also tell me about possible options to include > HETATM groups > from templates to the model? > > E.g both of my templates have two HETATM groups; from GFP > protein its > chromophore group which is covalently bonded to the > polypeptide chain > (like retinal in rhodopsin or HEM in globins) of that > protein. > from the second globular domain- its small cyclic GMP > molecule which > is the diffusive ligand of that protein. > > In the final model I'd like to include both of the groups > from both of > the templates (chromophore to the GFP part as well as cGMP > to the > interior of the second protein). > > By the way should I define chromophore group as the part of > the first > (gfp) as well as 3rd (output fussed chimera) sequence or > there is > another way to its inclusion ? > > Thanks for help again, > > James > > 2012/12/10, flavio seixas <oivalf_nix(a)yahoo.com>: > > Hi James, > > > > Modeller results are reproducible. I see you are > producing just one model. > > Each time you run your script, it will produce the same > model with the same > > error. > > > > Try to run more models and compare them. Try at least > 100. I usually > > produces 1000 and select the best by modeller dope > score and procheck > > evaluation. > > > > First of all, try to correct your alignment file. > > > > Your alignment file still incorrect (see attached). I > see that in your file, > > the sequences are: > > > > > > aaaaaa------* > > ----bbbbbbb* > > ccccccccccccccc* > > > > > > All sequences must have the same length! > > > > Maybe this is a problem with your text editor. Try to > use Nedit (for linux). > > This editor does not have limits for number of columns > and does not break > > the lines. > > > > I suggest you use Uniprot tab for alignment > (www.uniprot.org) > > > > You can display the alignment in fasta or pir format. > > > > regards, > > > > Flavio > > > > > > > > > > --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 7:26 AM > >> Flavio, > >> > >> below you could find my script as well as new > alignment > >> file. That > >> inpud data produces still wrong result in the > conformation > >> of second > >> template > >> > >> # 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 = 'align-multiple.ali', # alignment > filename > >> > >> knowns = ('1gfl', '3u10'), > >> # codes of the templates > >> sequence = > >> 'seq') > >> # code of the target > >> automodel.initial_malign3d= True > >> 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 > >> > >> > >> >P1;1gfl > >> structureX:1gfl:1 ::238 : :::-1.00:-1.00 > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* > >> > >> >P1;3u10 > >> structureN:3u10:470 :A:671 : :A::-1.00:-1.00 > >> > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASM > >> > PLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASV > >> RADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* > >> > >> >P1;seq > >> sequence:seq: : : > >> : ::: 0.00: 0.00 > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH* > >> > >> > >> by the way do you know any web servers for > produccing such > >> multiple > >> ali files for modeller input like > >> aaaa---- > >> ----bbbb > >> > >> for protein aaaabbbb > >> ? > >> > >> ( the above file I've done manually) > >> > >> James > >> > >> > >> 2012/12/9, flavio seixas <oivalf_nix(a)yahoo.com>: > >> > 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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Re: [modeller_usage] Protein-ligand simulate annealing
by flavio seixas 10 Dec '12

10 Dec '12

Hi Ben? I found the most answers to my previous questions at http://salilab.org/modeller/FAQ.html#8 The Charmm parameter and topology for ligand were successfully generated with all Hydrogens by swissparam server. I follow the instructions and edit the files: top_heav.lib, radii.lib, radii14.lib, solv.lib and restyp.lib, where my ligands were defined has one letter code "8". See the end of the alignment (*.pap): _aln.pos 270 280 290 1HVY KIDDFKAEDFQIEGYNPHPTIKMEMAV8 TS-Tgondii EIDDFTAEDFEVVGYVPHGRIQMEMAV8 _consrvd **** **** ** ** * ****** After build models with "allhmodel" options, i saw that the ligand in models remains unchanged. Its like It was defined it as BLK "." Ligand position and interactions were not optimized. All amino acids residues have hydrogens but the ligand not, in spite of all ligand hydrogens are present in its topology at top_heav.lib. Which file must I edit to set the parameter for lgiand? par.lig, par_all22_prot_b5.inp or par19.inp? What is missing? Regards, Flavio --- On Thu, 12/6/12, flavio seixas <oivalf_nix(a)yahoo.com> wrote: > From: flavio seixas <oivalf_nix(a)yahoo.com> > Subject: [modeller_usage] Protein-ligand simulate annealing > To: "Modeller Usage" <modeller_usage(a)salilab.org> > Date: Thursday, December 6, 2012, 7:17 PM > Hi Ben > > I successfully generate charmm force fields (parameter and > topology files) using swissparam server, for the ligand that > is bonded to my protein template. > > Now I want to built models bonded to this ligand and also > optimize them using Modeller protocol for MD and SA. > > My questions are: > > 1) How can I make modeller reads the parameter and topology > files for the ligand? Is there a command for it? > > 2) Or should I copy and paste the ligand topology data to > top_heav.lib file? > > 3) If the second option is the choice, where to paste the > information regarding the parameters? > > 4) In the alignment file, how to set the symbol for the > ligand? I think if I set it as BLK "." no changes will be > made. Is that right? > > Best regards, > > Flavio > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >

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