[Chimera-users] Distance between atoms at the interface

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 22 17:55:20 PDT 2013

Dear Mehdi,
If you can express the cutoff as a distance between the atoms' VDW surfaces instead of as a distance between their centers, this is easily done using the "Find Clashes/Contacts" tool (in menu under Tools... Structure Analysis) or "findclash" command.


For these, the relevant cutoff is called the "overlap": 0 overlap means the surfaces are touching, positive values means they are overlapping or clashing, and negative values are separated in space.  You would want to specify a negative overlap cutoff with zero H-bond allowance, for example to identify contacts between chains A and B with VDW surfaces within 2 angstroms:

findclash :.a test :.b overlap -2 hbond 0 log true

By default, results are shown with lines. The lines are only shown when their atoms are shown, so to make sure you see all the lines, you may want to display all atoms (for example, command: display). You can also write out a list of the atom pairs, overlap values, and center-center distance values; the example sends this info to the Reply Log (show using Favorites menu), but another possibility is to write a file.  You can filter by the center-center distance if you really wanted to use that criterion rather than VDW overlap.  The example command found 308 contacts for 4hhb, with Reply Log showing:

Allowed overlap: -1
H-bond overlap reduction: 0
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True

308 contacts
atom1  atom2  overlap  distance
PRO 114.A O    HIS 116.B NE2  0.396  2.664
HIS 103.A CE1  GLN 131.B OE1  0.299  2.881
ARG 31.A NH1   GLN 127.B OE1  0.253  2.807
PHE 117.A O    ARG 30.B NH2   0.249  2.811
ARG 31.A CD    GLN 127.B OE1  0.231  3.069
PRO 114.A CA   HIS 116.B NE2  0.225  3.295
HIS 122.A ND1  ARG 30.B NH1   0.225  3.055
[... etc. ...]
VAL 107.A CB   ALA 115.B CB   -0.992  4.752
PRO 119.A CA   ARG 30.B NH2   -0.995  4.515
ALA 111.A CA   GLY 119.B C    -0.998  4.488

These are in order of decreasing overlap, so the longest distances will be at the end.  In this case, you can see that using a -2 overlap cutoff gives distances >4 angstroms.  If you really want all distances up to 6, which may be a LOT of output, you could try a more negative overlap cutoff.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 21, 2013, at 7:31 PM, Mehdi Talebzadeh Farooji wrote:

> Dear Chimera Users,
> I was wondering if there is a way to show distances between two objects (two chains) and filter them; for instance to display all of the distnaces between atomes of two interacting protein chains which are less than 6 A.
> Any help would be much appreciated,
> Mehdi

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