king-probe(1) Evaluate and visualize protein interatomic packing


Syntax: probe input.pdb >> out.kin
or: probe [flags] "src pattern" ["target pattern"] pdbfiles... >> out.kin


self intersection: src -> src (default)
intersect both ways: src <=> targ
single intersection: src -> targ
external van der Waals surface of src (solvent contact surface)
-AUTObondrot filename
read and process an autobondrot file
<<NO FLAGS>>same as: -4H -mc -het -self "altA ogt33"
same as: <<NO FLAGS>>, but allows some other flags
-SCSurface same as: -drop -rad1.4 -out "not water"
same as: -drop -rad1.4 -out (note: user supplies pattern)
same as: -drop -rad0.0 -add1.4 -out "not water"
same as: -drop -rad0.0 -add1.4 -out (note: user supplies pattern)
-SCAN0 same as: -4H -mc -self "alta blt40 ogt33"
-SCAN1 same as: -4H -once "sc alta blt40 ogt33" "alta blt40 ogt65,(not water ogt33)"
count the atoms in the selection: src
(note that BOTH and ONCE require two patterns while
OUT, SELF and DUMPATOMINFO require just one pattern)
implicit hydrogens
explicit hydrogens (default)
set dot density (default 16 dots/sq A)
set probe radius (default 0.25 A)
offset added to Van der Waals radii (default 0.0)
-SCALEvdw#.# scale factor for Van der Waals radii (default 1.0)
scale C=O carbon Van der Waals radii (default 0.94)
draw spike instead of dots (default)
set spike scale (default=0.5)
draw only dots
-HBRegular#.# max overlap for regular Hbonds(default=0.6)
-HBCharged#.# max overlap for charged Hbonds(default=0.8)
keep nonselected atoms (default)
drop nonselected atoms
limit bump dots to max dist when kissing (default)
do not limit bump dots
add lens keyword to kin file
do not add lens keyword to kin file (default)
include mainchain->mainchain interactions
include dots to non-water HET groups (default)
exclude dots to non-water HET groups
include dots to water (default)
exclude dots to water
show dots between waters
include water H? vectorlist in output
extend bond chain dot removal to 4 for H (default)
limit bond chain dot removal to 3
limit bond chain dot removal to 2
limit bond chain dot removal to 1
-IGNORE "pattern" explicit drop: ignore atoms selected by pattern
recognize CH..O Hbonds
scale factor for CH..O Hbond score (default=0.5)
use short radii of polar hydrogens (default)
do not shorten radii of polar hydrogens
-NOFACEhbond do not identify HBonds to aromatic faces
-Name "name" specify the group name (default "dots")
group name used as extra master={name} on lists
do not generate @group statement in .kin format output
add @kinemage 1 statement to top of .kin format output
produce a count of dots-not a dotlist
output raw dot info
name:pat:type:srcAtom:targAtom:mingap:gap:spX: spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval:
output dot info formatted for display in O
output dot info formatted for display in XtalView
output one line :contacts:by:severity:type:
color dots by gap amount (default)
color dots by atom type
color dots by nucleic acid base type
color dots by gap and nucleic acid base type
-OUTCOLor "name" specify the point color for -OUT (default "gray")
set weight for scoring gaps (default 0.25)
-BUMPWeight# set relative scale for scoring bumps (default 10.0)
set relative scale for scoring Hbonds (default 4.0)
Division for Bump categories (default -0.4)
Division for Contact categories (default 0.25)
Occupancy below this is same as zero (default 0.02)
add master buttons for different elements in kin output
do not output contacts for HBonds
do not output contacts for clashes
do not output contacts for van der Waals interactions
onlybadout output bad clashes (severe overlap contacts)
output summary list of contacts and clashes
output summary list on oneline
do not display the residue name ticker during processing
assume only standard bonding patterns in standard residues
do not bond hydrogens based on table of parent heavy atoms
use the PDB SegID field to descriminate between residues
generate old style -u output: kissEdge2BullsEye, etc
verbose mode (default)
display reference string
display a list of program changes
quiet mode
show expanded help notice (includes other flags)
one line version to stdout

Pattern elements: (should be put in quotes on the command line)

within file #
within model #
within chain a
segment identifier aaaa (where _ represents blank)
alternate conformation a
atom name aaaa (where _ represents blank) (all 4 characters are used so H would be ATOM_H__)
residue aaa
residue #
residue #, insert a
residue range # (insert codes ignored)
residue type by one letter codes (eg. y)
residue type by three letter codes (eg. tyr)
all or a subset of the atoms
Occupancy less than # (integer percent)
Occupancy greater than # (integer percent)
B-value less than # (integer)
B-value greater than # (integer)
Insert code a (where _ represents blank)
WITHIN #.# OF #.#, #.#, #.#
atoms within distance from point
Patterns can be combined into comma separated lists such as "trp,phe,tyr" meaning TRP or PHE or TYR.
Patterns that are sepatated by blanks must all be true such as "chainb 1-5" meaning residues 1 to 5 in chain B.
You can also group patterns with parenthesis, separate multiple patterns with | meaning 'or' and choose the complement with NOT as in "not file1" meaning not in file 1.
An autobondrot file is similar to other PDB input files but it includes information identifying atoms subject to rotations and other transformations.
Example autobondrot file fragment showing Calpha-Cbeta bond rotation and a periodic torsion penalty function for this rotation
1 CB TYR 61 34.219 17.937 4.659 1.00 0.00
0:359:5:33.138:18.517: 5.531:34.219:17.937: 4.659
cos:-3:60:3: ATOM 1 1HB TYR 61 34.766 18.777 4.206 1.00 0.00 ATOM 1 2HB TYR 61 34.927 17.409 5.315 1.00 0.00 ATOM 1 CG TYR 61 33.836 16.989 3.546 1.00 0.00 ...
Autobondrot commands use colons to separate values Transformations: BONDROT:id:currAng:start:end:stepSz:x1:y1:z1:x2:y2:z2
# dummy
Bias functions:
COS:scale:phaseOffset:frequency POLY:scale:offset:polynomialDegree CONST:value
SAVE and RESTORE or "(" and ")"
(e.g. to rotate each Chi and the methyls for isoleucine the
sequence is: rotChi1/SAVE/rotChi2/rotCD1/RESTORE/rotCG2)
Set orientation: GO:angle1:angle2:... Include files: @filename Comments: # comment text

probe: version 2.13.110909, Copyright 1996-2011, J. Michael Word