On Thu, Nov 13, 2008 at 12:00 AM,
<modeller_usage-request@salilab.org> wrote:
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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)
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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
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