User:Wayne Decatur/I-Ppo Morph Methods: Difference between revisions
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I loaded 1a73 structure into [http://spdbv.vital-it.ch/ Swiss-pdb viewer (DEEP VIEW)] and let it magic fit the apo enzyme in 1evx. I disabled movement on those two structures and loaded the unbound DNA. When I had turned it so it was close, I enable movement on all and turned about 90 degrees and then disabled movement again all all but the unbound DNA and moved it into plane with the other structures. I save each layer individually. I edited the aligned 1evx file to match atom numbers with the aligned 1a73 and removed the SO4s. I deleted the 2 Magnesiums in the aligned 1a73 file. | I loaded 1a73 structure into [http://spdbv.vital-it.ch/ Swiss-pdb viewer (DEEP VIEW)] and let it magic fit the apo enzyme in 1evx. I disabled movement on those two structures and loaded the unbound DNA. When I had turned it so it was close, I enable movement on all and turned about 90 degrees and then disabled movement again all all but the unbound DNA and moved it into plane with the other structures. I save each layer individually. I edited the aligned 1evx file to match atom numbers with the aligned 1a73 and removed the SO4s. I deleted the 2 Magnesiums in the aligned 1a73 file. | ||
Next, I needed to renumber the atoms in the unbound DNA to make it easy to compare to file 1a73 | Next, I needed to renumber the atoms in the unbound DNA to make it easy to compare to file 1a73 so that I could match up the 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 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 | (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 the file and learned it wasn't what I want; however, here is the program I wrote in case anyone else needs a program that alters residue numbers using Biopython: | ||
the program that | |||
<pre> | <pre> | ||
