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2125 Views 4 Replies Latest reply: Mar 29, 2012 10:52 AM by diana.drennan RSS
Currently Being Moderated

May 10, 2011 5:31 AM

Possibility to determine clashing atoms?

Dear all,


imagine you have any dimer consisting of subunits A and B whereas A is partially in contact with B.

Furthermore, let's assume that you have superimposed any other subunit (from a different PDB file),

let's say C, on B and visualizing solely C and A in DS using CPK "looks good/fits pretty well". Anyways.

My question is: Is there any possibility in DS (free version) to determine whether there are atomic

clashes between A and C (e. g. by breaking vdW radii)? If so, how can I determine/visualize them?


Thanks a lot in advance,


  • yeh Accelrys 154 posts since
    May 10, 2006
    Currently Being Moderated
    May 16, 2011 2:07 PM (in response to Anders)
    Possibility to determine clashing atoms?

    Yes, in DS Visualizer, you can use the menu command Structure > Monitor > Bumps.


    You can find detailed information on Bump monitors from the DS Help online document.


    The Bump monitor displays close inter-atomic contacts between the selected atoms, or between all atoms if no atoms are selected. The Bump monitors display will be updated interactively.


    By default a Bump monitor will display if the distance between the two atoms is less than 70% of the sum of the two atoms’ van der waals radii. User can modify this default percentage value: From the Data table, BumpMonitor tab, set the ‘VDW Percent’ value. By default, bumps are displayed as magenta dashed lines, user can change the color as well.


    Hope this helps.

    • diana.drennan Active Contributor 14 posts since
      Jan 7, 2008
      Currently Being Moderated
      Mar 28, 2012 4:06 PM (in response to yeh)
      Possibility to determine clashing atoms?

      Is there a script that will list them for me ?  similar to the "" script lists the h-bonds ?  I like one for pi-pi bonds too.  I'd REALLY love it if I could have the script run over the output of an in-situ minimization run for me.....   =)

      • yeh Accelrys 154 posts since
        May 10, 2006
        Currently Being Moderated
        Mar 28, 2012 6:32 PM (in response to diana.drennan)
        Possibility to determine clashing atoms?

        The list of data are available in the Data table, in the Bump tab.

        After putting on the Bumps monitor, the Data table would have several tabs added. In the Bump tab, the Name column contains the list of atom pairs, and the Distance column contains the corresponding distances. e.g.




        Similarly, after putting on the Pi Interactions monitor, see the “Pi Interaction Pair” tab in the Data table. e.g.



        The data from the appropriate tab in the table can be saved to a csv file using File | Save As, select the file type Comma Separated Files (*.csv).


        Hope this helps.

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