User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions
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And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb'<br> | And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb'<br> | ||
'''However, that didn't save orientation I expected.''' I tried it on a single pdb file (no multiple models in the file) that I did rotate and instead of using 'all' as the name I used the object ('save_transformed 3KG2a, test.pdb') and it did save it as a different orientation; however, strangely not the exact one I expected. '''There must be an error in how the matrix is applied or the script is old and the matrix was altered | '''However, that didn't save orientation I expected.''' I tried it on a single pdb file (no multiple models in the file) that I did rotate and instead of using 'all' as the name I used the object ('save_transformed 3KG2a, test.pdb') and it did save it as a different orientation; however, strangely not the exact one I expected. '''There must be an error in how the matrix is applied or the script is old and the matrix was altered after.''. Yet since each of the ten models in the subunit A to B morph would need to be changed individually, it wouldn't be worth it when Jmol can fix it right after it loads. | ||
'''Problem was earlier in PyMol that I was orienting the view the way I wanted but not actually changing orientation of molecule.''' To move one molecule to where I want and change coordinates I really need to just go into the 3-butting editing mode and while holding down the SHIFT BUTTON, rotate the molecule to where I want, and then save from the main menu. This is similar to how it tells you to superimpose by hand according to [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page of the PyMol Wiki]. Except I don't have a real other molecule there. I just have a vision of where I want the molecule to be. Now to test of I can load the subunit a to b morph and get the correct file back out?<br> | '''Problem was earlier in PyMol that I was orienting the view the way I wanted but not actually changing orientation of molecule.''' To move one molecule to where I want and change coordinates I really need to just go into the 3-butting editing mode and while holding down the SHIFT BUTTON, rotate the molecule to where I want, and then save from the main menu. This is similar to how it tells you to superimpose by hand according to [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page of the PyMol Wiki]. Except I don't have a real other molecule there. I just have a vision of where I want the molecule to be. Now to test of I can load the subunit a to b morph and get the correct file back out?<br> | ||
