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coot [2009/01/08 10:13]
landon
coot [2009/01/08 10:25]
landon
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     * This is not the alpha carbon, it's the one connected to the oxygen     * This is not the alpha carbon, it's the one connected to the oxygen
   * Click on the // add residue // tool then on the carbon atom   * Click on the // add residue // tool then on the carbon atom
-    * Coot attempts to add a new residue that fits the electron density map +    * Coot attempts to add a new residue that fits the electron density map. This initial placement is usually junk because the reason the author didn't include the residue in the first place is because the electron density here is too spread out. Also, refinement steps may have removed the electron density here completely. 
-    * Move the residue ​to make it be close enough to bond to the carbon atom +    * Move the residue close enough to bond to the carbon atom 
-  * Click on the // regularize zone // tool then on the new residue ​to orient it such that it makes sense while ignoring the electron density map +  * Click on the // regularize zone // tool then on the new residue 
-  * Don't forget ​to save+    * This idealizes the residue'​s geometry ​while ignoring the electron density map 
 +  * Choose // File -> Save Coordinates// ​to save
  
 ==== 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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