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

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 6 09:31:16 PDT 2016


Hi Jiying Jia,
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
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2016, at 6:38 AM, xibei <zhuceyonghu123 at 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

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