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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)
Message: 1 Date: Tue, 13 May 2008 12:49:35 -0400 From: Juan Chang <">>
Subject: [modeller_usage] EM density maps for building models? To: "> Message-ID: <">>
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!
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Message: 2 Date: Tue, 13 May 2008 12:28:44 -0700
From: Modeller Caretaker <">> Subject: Re: [modeller_usage] EM density maps for building models? To: Juan Chang <">>
Cc: "> Message-ID: <">> 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.
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).
Message: 4 Date: Thu, 22 May 2008 12:24:33 +0530 From: "deepti nayar" <">> Subject: [modeller_usage] multiple template model
To: "> Message-ID: <">>
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.
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???
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"?