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coot [2009/01/08 10:19]
landon
coot [2009/01/08 10:25] (current)
landon
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 ==== Duplicating a portion of a molecule onto another molecule ==== ==== Duplicating a portion of a molecule onto another molecule ====
-Suppose you've got two PDB files and each are missing the last few residues. You want to insert the residues ​into both & have them match exactly+Suppose you have two PDB files of the same protein in different conformations but one is missing the last few residues. You want to insert the residues ​and have this section of the protein ​match exactly ​between the two PDB files. 
-  * Load both PDB files into Coot +  * In [[PyMol]] load the protein with the residues ​to be copied. 
-  * Insert residues into one of the proteins and get them looking how you want +  * Make a new PDB file that is just these residues and the residue they connect to. 
-  * Save and close this protein +  * Load this PDB file and the file that is to receive the residues ​into Coot. 
-  * In [[PyMol]] load the protein with the new residues. Make a new PDB file that is just the newly inserted ​residues and the residue they connect to. Load this PDB file into Coot. +  * In Coot choose // Calculate -> LSQ superpose // and align the molecule and the fragment using the common ​residue ​between ​the two 
-  * In Coot choose // Calculate -> LSQ superpose // and align the molecule and the fragment using the residue ​right before ​the new residues +  * Delete the common ​residue ​from the fragment
-  * Delete the connecting ​residue+
   * Choose // Calculate -> Merge Molecules // to merge the two into one molecule   * Choose // Calculate -> Merge Molecules // to merge the two into one molecule
   * Choose // File -> Save Coordinates // to save this new molecule   * Choose // File -> Save Coordinates // to save this new molecule

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