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Recipe: Atom Number Identifier v1.0.1 -- Brow42
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Name: Atom Number Identifier v1.0.1 -- Brow42
ID: 39989
Created on: Fri, 03/23/2012 - 17:43
Updated on: Sat, 03/24/2012 - 05:45
Description:

1) go to view-atom mode 2) make a small number of bands on a small number of segments (< 3). Select or freeze the segments. 4) Run script to get atom numbers.



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brow42's picture
User offline. Last seen 2 weeks 21 hours ago. Offline
Joined: 09/19/2011
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Tag atoms with rubber bands, get their number

This script will loop through all the atoms of a segment, looking for ones that have bands attached. It doesn't know which segment to check, so you have to mark them using selection interface or freezing them (backbone or sidechain). The more you select, the more atoms will be tested for each band you have made, so test 3 segments at a time.

To identify the number of an atom, make a band from it, freeze or select the segment, and run the script. You can make multiple bands on multiple segments; output will be in the order the bands were created.

Program will output the segment and atom numbers for the STARTING point of each band you have made (doesn't matter where the other end is). Note that the first and last segments of a polypeptide have different atom numbering due to extra atoms.

This script is just a temporary measure. Eventually all the information should be in a table, like the old hydrophobe table. The script will still be useful for non-amino-acid ligands.

To see atoms, go to (advanced) View, pick Stick + H or Polar H. Set the coloring to CKY. Blue = Nitrogen (#1 on the backbone), grey/other = C, Red = Oxygen, White = Hydrogen. Polar H only shows hydrogens attached to a hydrogen bond donor.

Keyboard shortcut: Ctrl-Shift-V

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons