Dear developers,

Why still there is no gui for modeller.

S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.

On Thu, Nov 13, 2008 at 12:00 AM, modeller_usage-request@salilab.orgwrote:

> Send modeller_usage mailing list submissions to > modeller_usage@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@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@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: interpolating missing residues (Modeller Caretaker) > 2. Re: modeling of phosphorylated polypeptide (Modeller Caretaker) > 3. Re: modeling of phosphorylated polypeptide (Modeller Caretaker) > 4. How to install pylab in modeller? (vidhya ganesh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Nov 2008 20:38:24 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] interpolating missing residues > To: BIN ZHANG zhngbn@gmail.com > Cc: modeller_usage@salilab.org > Message-ID: 491A5DC0.2090509@salilab.org > Content-Type: text/plain; charset=ISO-8859-1 > > BIN ZHANG wrote: > > I was trying to add missing residues in pdb file according to the page: > > > > http://salilab.org/modeller/wiki/Missing%20residues > > > > But, one thing I don't understand is how can I get the "alignment.ali" > file? > > You have to create it manually. You can add the missing residues by > reading the REMARK lines in the PDB to figure out which ones are > missing, and then perhaps the SEQRES lines to figure out what the > residue types are. > > > Aslo, it seems to me the command complete_pdb() can also do the job? > > http://salilab.org/modeller/manual/node403.html > > Is this true? If so, what's the difference between these 2? > > No - complete_pdb does not add missing residues. It adds any missing > *atoms* for any residue - for example, if your input PDB contains only > CA coordinates, it will add (using internal coordinates) the rest of the > backbone and sidechain. But it won't add any residues that aren't in the > PDB in the first place. > > 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, 11 Nov 2008 22:32:20 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide > To: xpzhang@ucdavis.edu > Cc: modeller_usage@salilab.org > Message-ID: 491A7874.6010100@salilab.org > Content-Type: text/plain; charset=ISO-8859-1 > > Xiao-Ping Zhang wrote: > > Many proteins are phosphorylated in vivo and and the status of their > > phosphorylation correlate to their function. The residues which are > > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > > I wonder how to build a phosphorylated model directly or how to apply a > > patch on a model to get a phosphorylated model in Modeller? > > Sure - you could build a comparative model in the usual way (assuming > you have a template) and phosphorylate the residues you're interested in > by applying a suitable patch in the special_patches method. If a > suitable patch does not exist, you'll have to add a new one to the > topology file - see the FAQ or the CHARMM forums. > > If your intention is to take an existing PDB and use Modeller to > phosphorylate some residues, Modeller is perhaps not the best package > for the job - you'd be better off using a dedicated MD program. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 3 > Date: Tue, 11 Nov 2008 22:36:13 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide > To: Dibyabhaba Pradhan dbpinfo@gmail.com > Cc: modeller_usage@salilab.org > Message-ID: 491A795D.10104@salilab.org > Content-Type: text/plain; charset=ISO-8859-1 > > Dibyabhaba Pradhan wrote: > > I modelled number of proteins by basic modelling. After basic > > modelling during procheck evaluation the residues in most favorable > > region is generally above 90% but after loop refinement the residues > > in most favorable region comes below 90%. Please kindly inform me what > > may be the region for this. > > > > Also after energy minimization the the percentage of residue in most > > favorable region decreses. > > I'm not sure what this has to do with phosphorylation, but there is > certainly no guarantee that a single minimization will give a "better" > model. You'd be better off building several models to get a reasonable > sampling of the energy landscape and then picking the best cluster or > single model. > > 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: Wed, 12 Nov 2008 14:33:40 -0800 (PST) > From: vidhya ganesh vidhya_81in@yahoo.com > Subject: [modeller_usage] How to install pylab in modeller? > To: modeller_usage@salilab.org > Message-ID: 499646.88880.qm@web34203.mail.mud.yahoo.com > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > In Model evaluation, I installed matplotlib inorder to build the plot > between my template and model , but I can't find pylab, which I > think is a submodule under matplotlib.? All of the > documentation for matplotlib starts with "from pylab import *", but > this of course doesn't work. > > Is pylab included in the distribution? > If not, is there a use for matplotlib _without_ pylab? > > Thanks > > Vidhya > > > > >