The “findclash” default is to ignore interactions between atoms that are separated by 4 or fewer bonds, and this is controlled by the “bondSeparation” option.  For example, to ignore only interactions between pairs of atoms that are directly bonded (separated by 1 bond), you would use a command something like:

findclash #0 test #0 bondSep 1

… giving results shown in attached image, except I changed the line colors afterwards.

You can use command “help findclash” to see the findclash manual page (which explains the options and their default values), or see it on our website here:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

I hope this helps,

Elaine
On Jul 6, 2016, at 6:38 AM, xibei <zhuceyonghu123@126.com> wrote:

Hi,
I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap?

Example molecular (init.mol2):
@<TRIPOS>MOLECULE
init.mol2
20 19 20 0 0
NUCLEIC_ACID
NO_CHARGES


@<TRIPOS>ATOM
      1 C          14.7888   10.0072   -5.6663 C.3       1  DA    0.0000
      2 C          15.4013    8.5150   -3.5012 C.3       2  DA    0.0000
      3 C          13.7388    8.7698   -5.6133 C.3       3  DA    0.0000
      4 C          14.6414    7.5770   -3.3654 C.3       4  DA    0.0000
      5 C          12.9675    5.9273   -2.0359 C.3       5  DA    0.0000
      6 C          13.6457    4.0155   -0.2544 C.3       6  DA    0.0000
      7 C          12.8822    2.8588    2.0634 C.3       7  DA    0.0000
      8 C          11.7541    3.3958    4.4562 C.3       8  DA    0.0000
      9 C          11.2290    4.5854    6.8231 C.3       9  DA    0.0000
     10 C          13.8907    4.6510    7.2730 C.3      10  DA    0.0000
     11 C          15.5581    5.2490    9.3114 C.3      11  DA    0.0000
     12 C          17.8150    4.7800   10.7177 C.3      12  DA    0.0000
     13 C          18.0666    2.1205   10.3271 C.3      13  DA    0.0000
     14 C          16.9288    4.4119    9.4640 C.3      14  DA    0.0000
     15 C          14.9471    3.0788   10.7232 C.3      15  DA    0.0000
     16 C          16.7345    3.9070    8.8773 C.3      16  DA    0.0000
     17 C          15.5384    2.3512   10.7314 C.3      17  DA    0.0000
     18 C          16.0476    1.4159    8.2501 C.3      18  DA    0.0000
     19 C          17.5152    1.5369    5.9877 C.3      19  DA    0.0000
     20 C          17.5650    3.1811    3.8468 C.3      20  DA    0.0000
@<TRIPOS>BOND
     1    1    2 1
     2    2    3 1
     3    3    4 1
     4    4    5 1
     5    5    6 1
     6    6    7 1
     7    7    8 1
     8    8    9 1
     9    9   10 1
    10   10   11 1
    11   11   12 1
    12   12   13 1
    13   13   14 1
    14   14   15 1
    15   15   16 1
    16   16   17 1
    17   17   18 1
    18   18   19 1
    19   19   20 1
@<TRIPOS>SUBSTRUCTURE
     1  DA     1 RESIDUE           4 A      DA     1 ROOT
     2  DA     2 RESIDUE           4 A      DA     2
     3  DA     3 RESIDUE           4 A      DA     2
     4  DA     4 RESIDUE           4 A      DA     2
     5  DA     5 RESIDUE           4 A      DA     2
     6  DA     6 RESIDUE           4 A      DA     2
     7  DA     7 RESIDUE           4 A      DA     2
     8  DA     8 RESIDUE           4 A      DA     2
     9  DA     9 RESIDUE           4 A      DA     2
    10  DA    10 RESIDUE           4 A      DA     2
    11  DA    11 RESIDUE           4 A      DA     2
    12  DA    12 RESIDUE           4 A      DA     2
    13  DA    13 RESIDUE           4 A      DA     2
    14  DA    14 RESIDUE           4 A      DA     2
    15  DA    15 RESIDUE           4 A      DA     2
    16  DA    16 RESIDUE           4 A      DA     2
    17  DA    17 RESIDUE           4 A      DA     2
    18  DA    18 RESIDUE           4 A      DA     2
    19  DA    19 RESIDUE           4 A      DA     2
    20  DA    20 RESIDUE           4 A      DA     1

Best Wishes!
Jiying Jia