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@hotmail.com Fone: +34645465174 (Spain)

On Aug 19, 2009, at 1:53 AM, modeller_usage-request@salilab.org wrote:

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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@salilab.org > To: albumns albumns@yeah.net > Cc: modeller_usage modeller_usage@salilab.org > Subject: Re: [modeller_usage] how to evaluate which is the best model > in "multiple template" example > Message-ID: 4A7AFBDB.3040400@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@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@sun.ac.za" storbeck@sun.ac.za > To: "modeller_usage@salilab.org" modeller_usage@salilab.org > Subject: [modeller_usage] Heme in P450 > Message-ID: > D698F2F3BBE7504AA43E6B2A7CFFD82D127FA65B14@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@salilab.org > To: "Storbeck, K, Dr storbeck@sun.ac.za" storbeck@sun.ac.za > Cc: "modeller_usage@salilab.org" modeller_usage@salilab.org > Subject: Re: [modeller_usage] Heme in P450 > Message-ID: 4A8B09C0.5030203@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Storbeck, K, Dr storbeck@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@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@caltech.edu > To: modeller_usage@salilab.org > Subject: [modeller_usage] remove short helices > Message-ID: 06A265F6-2F41-4968-86C3-C51B21041AA7@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@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 8, Issue 60 > *********************************************