On Thu, May 22, 2008 at 10:00 PM, <
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Today's Topics:
1. EM density maps for building models? (Juan Chang)
2. Re: EM density maps for building models? (Modeller Caretaker)
3. Modeller 9v4 release (Modeller Caretaker)
4. multiple template model (deepti nayar)
5. Re: multiple template model (Modeller Caretaker)
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Message: 1
Date: Tue, 13 May 2008 12:49:35 -0400
From: Juan Chang <juan.chang@bcm.edu>
Subject: [modeller_usage] EM density maps for building models?
To: modeller_usage@salilab.org
Message-ID: <4829C69F.6000108@bcm.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello,
The density.grid_search() function outputs a 'bestCC_targ' file which
contains the CCF. Is there a way to use this information for model
building? A web tutorial or Python code on how to use electron
microscope density maps for model building would be helpful.
Thanks!
------------------------------
Message: 2
Date: Tue, 13 May 2008 12:28:44 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] EM density maps for building models?
To: Juan Chang <juan.chang@bcm.edu>
Cc: modeller_usage@salilab.org
Message-ID: <4829EBEC.2030603@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Juan Chang wrote:
> The density.grid_search() function outputs a 'bestCC_targ' file which
> contains the CCF. Is there a way to use this information for model
> building? A web tutorial or Python code on how to use electron
> microscope density maps for model building would be helpful.
grid_search is for static fitting of models into density maps, e.g. for
model assessment. It is not suitable for guiding the model building
procedure itself. You could, however, check out Flex-EM at
http://salilab.org/Flex-EM/ and check out the referenced paper to see if
that is helpful for you.
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: Thu, 15 May 2008 09:17:30 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: [modeller_usage] Modeller 9v4 release
To: modeller_announce@salilab.org, modeller_usage@salilab.org
Message-ID: <482C621A.5030005@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The new version of Modeller, 9v4, is now available for download! Please
see the download page at http://salilab.org/modeller/ for more information.
If you have a license key for Modeller 8 or 9, there is no need to
reregister for Modeller 9v4 - the same license key will work. (It won't
do any harm to reregister if you want to, though!)
9v4 is primarily a bugfix release relative to the last public release
(9v3). Major user-visible changes include:
# The speed of GB/SA calculations has been dramatically increased.
# io_data.atom_files_directory is now a Python list of directories,
rather than a colon-separated string. (This is so that everything
works on Windows, where ':' is a valid character in directory names.)
Old scripts that use colon-separated strings should still work, but
will trigger a warning.
# When reading or writing compressed files, the uncompressed versions of
these files are now written into writeable local storage. Previously,
these files were written into the same directory as the compressed
versions, which is problematic when that directory is read-only or is
on network storage.
# Update PDB files used in the examples (remediated PDBs are now used).
See the Modeller manual for a full change log:
http://salilab.org/modeller/9v4/manual/node38.html
If you encounter bugs in Modeller 9v4, please see
http://salilab.org/modeller/9v3/manual/node10.html for information on
how to report them.
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: Thu, 22 May 2008 12:24:33 +0530
From: "deepti nayar" <deeptinayar@gmail.com>
Subject: [modeller_usage] multiple template model
To: modeller_usage@salilab.org
Message-ID:
<630ea2870805212354k4c5b5e5bmcb4cde2b08be5ca5@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi all
I am new to modeller. I am using modeller 9v2. I am trying to model
structure for a protein using two templates. Can anyone tell me
whethermodeller first builds its own alignment among the templates and then
build a model???
Is there a way by which we can get the model based on our wished alignment.
I tried this but it seems it doesnt work.
thanks
--
Regards
Deepti Nayar
Research Assistant
Bioinformatics Centre
National Institute of Immunology
New Delhi - 110067
e-mail: deeptinayar@gmail.com
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Message: 5
Date: Thu, 22 May 2008 09:29:51 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] multiple template model
To: deepti nayar <deeptinayar@gmail.com>
Cc: modeller_usage@salilab.org
Message-ID: <48359F7F.2030609@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
deepti nayar wrote:
> I am new to modeller. I am using modeller 9v2. I am trying to model
> structure for a protein using two templates. Can anyone tell me
> whethermodeller first builds its own alignment among the templates and
> then build a model???
You can certainly build models with multiple templates. There is even an
example in the manual: http://salilab.org/modeller/9v4/manual/node21.html
Modeller never 'automatically' builds an alignment - it takes the one
you give it. There are functions in Modeller to do alignments, however,
so you can use these to make your alignment if you want.
> Is there a way by which we can get the model based on our wished
> alignment. I tried this but it seems it doesnt work.
Sure, that's the default. Try running the example above to see for
yourself. What do you mean by "it doesn't work"?
Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
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