Tool: Clashes, Contacts
Clashes and Contacts are two separate tools with nearly
identical options. Some of the default parameters are different,
as meant to detect:
– unfavorable interactions where atoms are too close together;
– all kinds of direct interactions:
polar and nonpolar, favorable and unfavorable (including clashes)
The corresponding commands are
zone atom specification,
select by pseudobond length,
Protein-Ligand Binding Sites
Clashes and Contacts
can be opened from the Structure Analysis section of the
Tools menu and manipulated like other panels
Clicking Apply (or OK, which also dismisses the dialog)
runs the calculation. Several of the dialog settings are remembered as
preferences when the calculation is run.
Clicking Reset restores the dialog to factory default settings.
- Find pairs of atoms with:
- VDW overlap ≥ [ cutoff ] Å
(initial default on)
– identify pairs of atoms with VDW overlap ≥ cutoff.
The VDW overlap between two atoms is defined as the sum of their
VDW radii minus the distance between their centers.
An overlap of 0 means the VDW surfaces are just touching.
A positive overlap is how far the VDW surfaces interpenetrate, whereas a
negative overlap is the distance of separation between the VDW surfaces.
A larger positive cutoff restricts the results to more severe
clashes, whereas a negative cutoff can also identify
pairs of atoms that are farther apart.
...for Clashes only:
after subtracting [ allowance ] for H-bonding
– an allowance > 0 reflects the observation that
atoms sharing a hydrogen bond can come closer to each other
than would be expected from their VDW radii.
The allowance is only subtracted for pairs
comprised of a donor (or donor-borne hydrogen) and an acceptor.
This is equivalent to using smaller radii to characterize hydrogen-bonding
interactions (for example, see
and Nussinov, Proteins 32:111 (1998)).
As in H-Bonds,
possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms,
and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a
– OR –
- center-center distance ≤ [ d ] Å
(initial default off, with d=4.0)
– instead of VDW overlap,
use a simple distance cutoff to identify interactions
- Limit by selection (initial default off)
– whether to limit the results by the current
selection according to one of the following
choices in the pulldown menu:
- with at least one end selected
- with exactly one end selected
- with both ends selected
- between selection and atom spec...
The two sets of atoms may overlap, but will not overrule other restrictions.
- Ignore interactions between atoms [ N ] or fewer bonds apart
(initial default N=4)
- Ignore interactions between residues < [ M ] apart in sequence
(initial default off, with M=5)
- Include intermodel (initial default on)
- Include intramodel (initial default on)
- Include intramolecule (initial default on)
– whether to include intramolecular interactions,
where a molecule is defined as a covalently bonded set of atoms
- Include intraresidue (initial default off)
- Ignore hidden models (initial default on)
– ignore models that are hidden
at the model level
(e.g., with Model Panel
show/hide checkbox unchecked)
Treatment of results:
- Select atoms (initial default off)
– whether to select the interacting atoms
- Reveal atoms of interacting residues (initial default off)
– since a pseudobond
is only shown when both of its endpoint atoms are shown,
whether to ensure all showing all H-bonds by displaying all of the endpoint
atoms. To avoid showing disconnected atoms, the entire residues will be shown,
except that amino acid and nucleic acid residues are split into
moieties separately displayed by this option.
Displayed backbone atoms may still be invisible where cartoon is shown,
unless their simultaneous display has been enabled with
cartoon suppress false.
- Assign atomic attribute named [name]
(initial default off)
– whether to assign the largest overlap
per atom as an attribute with the
specified name (default overlap);
disallowed with continuous monitoring
- Display as pseudobonds (initial default on)
– whether to show the interactions as
pseudobonds, with related settings:
– pseudobond color
0.15 for clashes,
0.075 for contacts)
– pseudobond radius in Å
4 for clashes,
6 for contacts)
– pseudobond number of dashes;
currently, odd numbers are rounded down to give an even number of dashes.
- Distance label (initial default off)
– whether to show Å distances as bond labels;
the number of decimal places and whether to show the Å symbol can be
changed with distance style
or set beforehand in the
and label height in Å can be changed with
or set beforehand in the
The distances (pseudobond lengths) can also be plotted as a histogram with
- Group name
(initial default clashes or contacts according to
which tool is being used)
– name for the since a pseudobond group.
Pseudobonds with group name clashes can be removed with the command
clashes delete or
and those with group name contacts removed with
contacts delete or
A pseudobond model can also be closed
with the Model Panel
or the close command.
Write information to:
Where to write clash/contact information,
including atom pair specifications
(see the Labels preferences
for specifier style), overlaps, and center-center distances;
disallowed with continuous monitoring.
- Log (initial default off)
– show the information in the Log
- File (initial default off)
– save the information to a text file
Frequency of checking:
- when OK/Apply clicked (default)
continuously (until dialog closed)
– during motions
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