User:Wayne Decatur/I-Ppo Morph Methods: Difference between revisions
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Next, I needed to renumber the atoms in the unbound DNA to make it easy to compare to file 1a73 for matchin up number of atoms since morphing needs equal numbers. I also needed to change the chain ids from a and b to match c and d in 1a73. | Next, I needed to renumber the atoms in the unbound DNA to make it easy to compare to file 1a73 for matchin up number of atoms since morphing needs equal numbers. I also needed to change the chain ids from a and b to match c and d in 1a73. | ||
(At first, I thought Biopython would do this but after using the [http://biopython.org/DIST/docs/tutorial/Tutorial.html tutorial] to install | (At first, I thought Biopython would do this but after using the [http://biopython.org/DIST/docs/tutorial/Tutorial.html tutorial] to install Numpy1.1 and Biopython in addition to my already present installation of Python 2.5, I found at [http://maple.rsvs.ulaval.ca/mediawiki/index.php/Manipulating_PDB_files_using_BioPython the help site for manipulating pdb files with Biopython] and also the [http://biopython.org/DIST/docs/tutorial/Tutorial.html cookbook]that it doesn't concern itself with atom numbers that I could see and instead just parses all the other information like chain id and residue number to make that easy to work with. In fact I wrote a program with it to easily renumber residues and save file and learned it wasn't what I want - | ||
the program: | the program: | ||
