How do I installed Pylab for plotting the plot_profiles.py

On Thu, May 22, 2008 at 10:00 PM, modeller_usage-request@salilab.org wrote:

> 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. 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 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 >