User:Wayne Decatur/I-Ppo Morph Methods: Difference between revisions
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I loaded 1a73 structure into swiss-pdb viewer 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 degress 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 MGs in the aligned 1a73 file. | I loaded 1a73 structure into swiss-pdb viewer 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 degress 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 MGs 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 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 numpy 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 - | 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 numpy 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: | ||
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for model in structure:<br> | for model in structure:<br> | ||
for chain in model:<br> | <nowiki> | ||
for chain in model:</nowiki><br> | |||
i = 2493<br> | i = 2493<br> | ||
for residue in chain:<br> | for residue in chain:<br> | ||
