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Dear Crystallographers, Thanks very much for all who responded to my request. Below is a compiled list of the various ways to skin this crystallographic cat! Jacob -Moleman ca plot distance-CCP4's superpose-distance matrix analysis, e.g. http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html, or other programs-Lsqkab, with the "deltas" card-If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment. The sequence alignment will have an "RMSD" header running across the top, which is a bar graph of the RMSD values. You can the alignment's Headers->Save... menu item to save the numerical values to a file if you want. OR If you already have the structures superimposed on your own, you can use Chimera's Match->Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header.-Coot prints this information to the terminal, so you can start coot and 'tee' its output into a file.-Various fortran/homebrew programs available from individuals-LGA server: http://proteinmodel.org/AS2TS/LGA/lga.html On Tue, Nov 29, 2011 at 3:44 AM, Tim Gruene <[log in to unmask]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Jacob, > > Coot prints this information to the terminal, so you can start coot and > 'tee' its output into a file. > > Tim > > On 11/28/2011 11:53 PM, Jacob Keller wrote: >> Let me refine my question (sorry for my lack of clarity): is there a >> program that will output the distances between the corresponding ca's >> of a superposition on a residue-by-residue basis, and not just a >> global RMSD value (doubtless these numbers are part of the >> superposition algorithm itself)? I want to plot these values as a >> function of residue number to show which parts of the structures >> deviate more or less from each other. >> >> Jacob >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFO1KmAUxlJ7aRr7hoRAjy0AJ0WepnWXxMHVFfAE1oSX0rQ5BV4zQCggo/N > OQ67cZNE7jMPZyXL4v1zOjE= > =JXFJ > -----END PGP SIGNATURE----- -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [log in to unmask] *******************************************