[Chimera-users] crystal contacts to show molecules

Tom Goddard goddard at cgl.ucsf.edu
Mon Apr 28 13:46:20 PDT 2008

Hi Miguel,

  Chimera has several tools which help identify crystal contacts 
(Crystal Contacts, Unit Cell, Find Clashes/Contacts, and Multiscale 
Models).  Unfortunately this mish-mash has not yet been unified into a 
single simple to use crystal contact tool.  You can get all the 
contacting molecule copies using a combination of tools (in production 
release 1.2470).  Here's how:

  1) Open your pdb model (I tried 1a0m).
  2) Use menu entry Tools / Higher-Order Structure / Multiscale Models, 
select multimer type "3x3x3 crystal unit cells" near the bottom of the 
multiscale dialog and press the "Make models" button.
  3) Press the select "with loaded atoms" button at the top of the 
multiscale dialog to select the original molecule, adjust the contact 
"Range" near the top of the dialog, then press the "Near" button.
  4) Press the other chains "Hide" button to hide the non-contacting chains.
  5) Press the style "Show..." button and choose  "Wire" from the menu.
  6) Now you have all the molecules within the contact range.  Use menu 
entry Tools / Structure Comparison / Find Clashes/Contacts to draw lines 
between contacting atoms.  Press the left arrow keyboard key to return 
to selecting just the original copy of the molecule.  Press the 
"Designate" currently selected atoms button on the Find Clashes dialog, 
then press the Apply button on that dialog.  You may want adjust the VDW 
overlap and other Find Clash settings.  You can use a negative overlap 
if you want close atom pairs that are not in contact.

Some day we will have a much simpler interface to do these steps.


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