modeller_usage

modeller_usage@salilab.org

3151 discussions

Re: [modeller_usage] modeller_usage Digest, Vol 8, Issue 60
by carlos Prudencio 19 Aug '09

19 Aug '09

Hi, I need to do a de novo 3D model because I was't able to find any similar structural to compare. thanks, Carlos R. Prudencio MSN: crprudencio(a)hotmail.com Fone: +34645465174 (Spain) On Aug 19, 2009, at 1:53 AM, 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. Re: how to evaluate which is the best model in "multiple > template" example (Modeller Caretaker) > 2. Heme in P450 (Storbeck, K, Dr <storbeck(a)sun.ac.za>) > 3. Re: Heme in P450 (Modeller Caretaker) > 4. remove short helices (Shawna Frazier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Aug 2009 08:50:51 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: albumns <albumns(a)yeah.net> > Cc: modeller_usage <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] how to evaluate which is the best model > in "multiple template" example > Message-ID: <4A7AFBDB.3040400(a)salilab.org> > Content-Type: text/plain; charset=UTF-8; format=flowed > > albumns wrote: >> how to evaluate which is the best model in "multiple template" >> example? In the tutorial, it just use the model number 1 for the >> final one. How to judge these models which is better than the left? > > You can evaluate the model quality with the DOPE score (the model with > the lowest DOPE score is most likely to be the best) in the same way > as > the single template example. It doesn't matter how many templates were > used to build the model - the evaluation is of the model itself, not > the > alignment. > >> my another question is that how can we draw the "basic model" and >> multiple templates in the same diagram with GUNplot? > > If you're referring to the plot of DOPE score profiles, shown at the > end > of the basic tutorial, such a plot is only qualitative at best. You > can > only plot a single profile in GNUPLOT, because with multiple > profiles you have to account for the gaps. This is done by the > plot_profiles script in the basic tutorial. To plot multiple > templates, > it should be straightforward to modify that script, adding extra calls > to get_profile() and pylab.plot(). > > 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: 2 > Date: Tue, 18 Aug 2009 19:45:27 +0200 > From: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: [modeller_usage] Heme in P450 > Message-ID: > <D698F2F3BBE7504AA43E6B2A7CFFD82D127FA65B14(a)STBEVS06.stb.sun.ac.za> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am modeling a cytochrome P450, I am able to include the heme in my > model. However, in the templates the heme iron is bound to a cys > residue, but I loose this bond in the model. How can I go about > keeping it in my model? > > Thanks > Karl > > > ------------------------------ > > Message: 3 > Date: Tue, 18 Aug 2009 13:06:24 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Heme in P450 > Message-ID: <4A8B09C0.5030203(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Storbeck, K, Dr <storbeck(a)sun.ac.za> wrote: >> I am modeling a cytochrome P450, I am able to include the heme in my >> model. However, in the templates the heme iron is bound to a cys >> residue, but I loose this bond in the model. How can I go about >> keeping it in my model? > > If you have a CYS residue in your model aligned with that template > residue, then Modeller should automatically keep that bond in your > model > (see the third bullet point at > http://salilab.org/modeller/9v7/manual/node65.html). This does, > however, > require Modeller 9v5 or later. The heuristic is a simple one though > - if > the bond is longer than 2.3A you could just add a simple distance > restraint to approximate this interaction. But really to do this > properly you need to tell Modeller that that CYS residue is not > really a > 'CYS' but is a modified residue (i.e. that it has a bond to your > iron). > For that you'd need to patch your topology using the model.patch() > command and some knowledge of how CHARMM patches work, which can be > gleaned from the CHARMM manual. > > 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: Tue, 18 Aug 2009 16:38:21 -0700 > From: Shawna Frazier <sfrazier(a)caltech.edu> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] remove short helices > Message-ID: <06A265F6-2F41-4968-86C3-C51B21041AA7(a)caltech.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi, > > When I view my structural model as a cartoon, it contains several > short 'helices', composed of only three residues each. The template > pdb shows each of these regions as unstructured loops. Therefore, I > would like to remove these short helices from my model. Is there a > simple way to remove secondary structure? > > Note, I have tried loop refinement; it worked on a couple of my short > helices, but has failed to fix my last one. > > Any suggestions are appreciated. > Thanks. > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 8, Issue 60 > *********************************************

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Heme in P450
by Storbeck, K, Dr <storbeck＠sun.ac.za> 18 Aug '09

18 Aug '09

Hi, I am modeling a cytochrome P450, I am able to include the heme in my model. However, in the templates the heme iron is bound to a cys residue, but I loose this bond in the model. How can I go about keeping it in my model? Thanks Karl

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how to evaluate which is the best model in "multiple template" example
by albumns 06 Aug '09

06 Aug '09

Dear all: how to evaluate which is the best model in "multiple template" example? In the tutorial, it just use the model number 1 for the final one. How to judge these models which is better than the left? my another question is that how can we draw the "basic model" and multiple templates in the same diagram with GUNplot? Thank you very much.

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query about coil region!!
by Cool Hunk 05 Aug '09

05 Aug '09

Thanks alot Ben, i really got it, can you please make me one more thing sure that can i declare any part of my target a coil region irrespective of its alignment wth template region, if yes then how?? cuz in tht example its told about the helix n strand.... but not about coils... thanking in advance Muhammad

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query!!!
by Cool Hunk 04 Aug '09

04 Aug '09

Dear Ben, Actually i want to ask about a very common concept about modelling.... for this alignment, the red color representing beta strands is aligned with gaps and its the template part wch is aligned wth gaps, my question is how would this part be modelled??? would it be modelled a strand in predicted model??? and what if any part of target is aligned wth gaps but was conserdered a helix????? how would it be modelled.. --------000000000000000--------------------22--------------- CEEEEECCEEEEEEEEEEEEEEECCCCCCCCCCCC--------EECCEEEEEEEEEEECC AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGN--------GDMTYARLGFKGETQIN | | | -------MKKLLKSVLVFAALSSASSLQALPVGNPAEPSLMIDGIL-------------- -------CCCCCEEEEEEEEEEECCCCCCCCCCCCCEEEEEEEEEE-------------- Albeit its a childish question, but it can clear my concept and i can edit the alignment to get a good model then.. thanking in advance Muhammad

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refinement of model, but keeping close to templates
by Robert Jorissen 04 Aug '09

04 Aug '09

G'day I am modelling a complex of two proteins, each of which has moderately high sequence similarity to their respective template proteins. I wish to create a model that strongly resembles their targets. The idea being that I wish to demonstrate the plausibility of the interface between the two template proteins being conserved in the target proteins. What is the best way to go about this? Presently, I have created a number of models using the library_schedule autosched.fastest with a starting coordinate deviation of zero (i.e. no random displacement added to the initial set of coordinates) and taken the best scoring of these. Is there a better way that optimizes the MODELLER score, but that does not stray far from the template structure, particularly in the ungapped, high similarity regions? Kind regards, Rob Jorissen Ludwig Institute for Cancer Research, Melbourne branch ____________________________________________________________________________________ Access Yahoo!7 Mail on your mobile. Anytime. Anywhere. Show me how: http://au.mobile.yahoo.com/mail

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restraining bonds between het ligand and side chain atoms
by Violetta Kivovich 04 Aug '09

04 Aug '09

Hello, I am trying to introduce a restrain which would limit a bond length between a zinc and its coordinating side chain atom (N2 of His or O of Asn) in my model. I am not sure how to indicate the restraint in a script. Can you help? Thank you!

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Regarding energy minimization in modeller
by snoze pa 27 Jul '09

27 Jul '09

Hi, I am using modeller to build some homology model. But I am unable to find any script that can be used to minimize the structure. Is there any script available in modeller that can be used to energy minimize the modeled structure. I try to use the old script, model_energies.py but it give me following error message Traceback (most recent call last): File "model_energies.py", line 41, in ? mdl.generate_topology(aln, sequence=code+'-ini') TypeError: generate_topology() got an unexpected keyword argument 'sequence' How modeller can be used to energy minimize a model structure. I am using current version of modeller. Thank you very much. Sincerely, S

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Re: [modeller_usage] modeling a fragment of the target and template sequences
by bharat lal 21 Jul '09

21 Jul '09

Hi Sir, I was jus modeling the structure of 1fdx protein , taking the target 5fd1 (all these files are already there) but after running the script it closes all of a sudden in between and when modeling for the whole of the template and target sequence .. its giving structure .. So can u tell me where am i going wrong ?? and one more question .. If i am executing the script from the command line .. its not getting executed .. whereas a direct click on the script itself .. executes it .. thereby giving the structure ??? Now whats the problem here also .. Please guide .. Bharat See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/

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Introducing HETATM ligands into models based on multiple templates
by Violetta Kivovich 21 Jul '09

21 Jul '09

Hello, I am trying to create a model of a protein using 3 different templates. The first template covers about 1/3 of the protein, the second covers the central part of the model protein and the third overlaps with the second with an additional extension to cover the c- terminus of the protein. The templates' crystal structures have incorporated metal ions and other ligands, which i would like to transfer into the model. Unfortunately i cannot seem to make this work using the script for introducing HETATM ligands into the model. I have created the alignment file and added '.' into both the template and into the sequence alignment. The PDB has the HETATM ligands at the end of the sequence, so i have added them at the end of the alignment file, as suggested in the manual. However, since three different templates are being used, only parts of which overlap, introducing '.' at the end of the model sequence does not work, because it does not align with the template. On the other hand adding '.' into the model sequence, the way it would align with the template, disturbs the structure, disrupting the alignment with the other templates and causing a break in the peptide. I tried adding gaps for each ligand in the other templates, but this does not help. I have tried creating part of the model with just one template and the aligning sequence from my protein of interest. In that situation the ligands are easily added. Is there any remedy to my problem in modeller that i have not considered? here is the script i am using for introducing HETATM ligands into the model # Homology modeling with ligand transfer from the template 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'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = '1-78-40-clmpldr4.ali', # alignment filename knowns=('1M55','1U0J','1SXJ'), # codes of the templates sequence = 'B25') # 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 Violetta Kivovich MD/PhD Candidate G4 vzk102(a)psu.edu

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