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 and it did save it as a different orientation; however, strangely not the exact one I expected. Yet since it won't work with all, it wouldn't be worth it when Jmol can fix it right after it loads. | '''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 and it did save it as a different orientation; however, strangely not the exact one I expected. Yet since it won't work with all, it wouldn't be worth it when Jmol can fix it right after it loads. In fact, saving a layer from pymol after it had been pair_fit (PyMol moves the first object in a command like 'pair_fit 3KG2a,3KG2b' onto the second one does indeed change the orientation of the second one;note DeepView keeps what you loaded first in place and magicfits second item when magicftting default way so second orientation gets changed and saves different) and so they will be able to be superimposed in Jmol when superimposed that way. | ||
