[Chimera-users] About findclash in detecting overlap of atoms

[xibei]

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
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