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:
Fone: +34645465174 (Spain)
On Aug 19, 2009, at 1:53 AM, wrote:
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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 <>)
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 <>
To: albumns <>
Cc: modeller_usage <>
Subject: Re: [modeller_usage] how to evaluate which is the best model
in "multiple template" example
Message-ID: <>
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
--
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 <>" <>
To: "" <>
Subject: [modeller_usage] Heme in P450
Message-ID:
<>
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 <>
To: "Storbeck, K, Dr <>" <>
Cc: "" <>
Subject: Re: [modeller_usage] Heme in P450
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Storbeck, K, Dr <> 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
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
--
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 <>
To:
Subject: [modeller_usage] remove short helices
Message-ID: <>
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.
------------------------------
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End of modeller_usage Digest, Vol 8, Issue 60
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