User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions
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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 magic fits second item when magicfitting 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. | 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 magic fits second item when magicfitting 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. | ||
Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super] to be more | Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super here] to be more robust (and sequence-independent) than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL]. | ||
===In Jmol Application=== | ===In Jmol Application=== | ||
