---
name: "king-probe"
section: "1"
platform: "linux"
package: "king-probe"
version: "02.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/king-probe"
---

# king-probe(1)

Evaluate and visualize protein interatomic packing

## NAME

king-probe - Evaluate and visualize protein interatomic packing

## DESCRIPTION

Syntax: probe input.pdb \>\> out.kin

-

  or: probe \[flags\] "src pattern" \["target pattern"\] pdbfiles... \>\> out.kin

### Flags:

- **-SElf**

  self intersection:   src  -\> src (default)

- **-Both**

  intersect both ways: src \<=\> targ

- **-ONce**

  single intersection: src  -\> targ

- **-OUt**

  external van der Waals surface of src (solvent contact surface)

- **-AUTObondrot** filename

  read and process an autobondrot file

-

  shortcuts:

-

  \<\<NO FLAGS\>\>same as: **-4H** **-mc** **-het** **-self** "altA ogt33"

- **-DEFAULTs**

  same as: \<\<NO FLAGS\>\>, but allows some other flags

**-SCSurface** same as: **-drop** **-rad1**.4         **-out** "not water"

- **-EXPOsed**

  same as: **-drop** **-rad1**.4         **-out**      (note: user supplies pattern)

- **-ASurface**

  same as: **-drop** **-rad0**.0 **-add1**.4 **-out** "not water"

- **-ACCESS**

  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)"

- **-DUMPAtominfo**

  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**

  implicit hydrogens

- **-Explicit**

  explicit hydrogens (default)

- **-DEnsity**#

  set dot density (default 16 dots/sq A)

- **-Radius**#.#

  set probe radius (default 0.25 A)

- **-ADDvdw**#.#

  offset added to Van der Waals radii (default 0.0)

**-SCALEvdw**#.# scale factor for Van der Waals radii (default 1.0)

- **-COSCale**#.#

  scale C=O carbon Van der Waals radii (default 0.94)

- **-SPike**

  draw spike instead of dots (default)

- **-SPike**#.#

  set spike scale (default=0.5)

- **-NOSpike**

  draw only dots

**-HBRegular**#.# max overlap for regular Hbonds(default=0.6)

**-HBCharged**#.# max overlap for charged Hbonds(default=0.8)

- **-Keep**

  keep nonselected atoms (default)

- **-DRop**

  drop nonselected atoms

- **-LIMit**

  limit bump dots to max dist when kissing (default)

- **-NOLIMit**

  do not limit bump dots

- **-LENs**

  add lens keyword to kin file

- **-NOLENs**

  do not add lens keyword to kin file (default)

- **-MC**

  include mainchain-\>mainchain interactions

- **-HETs**

  include dots to non-water HET groups (default)

- **-NOHETs**

  exclude dots to non-water HET groups

- **-WATers**

  include dots to water (default)

- **-NOWATers**

  exclude dots to water

- **-WAT2wat**

  show dots between waters

- **-DUMPH2O**

  include water H? vectorlist in output

- **-4H**

  extend bond chain dot removal to 4 for H (default)

- **-3**

  limit bond chain dot removal to 3

- **-2**

  limit bond chain dot removal to 2

- **-1**

  limit bond chain dot removal to 1

**-IGNORE** "pattern" explicit drop: ignore atoms selected by pattern

- **-DOCHO**

  recognize CH..O Hbonds

- **-CHO**#.#

  scale factor for CH..O Hbond score (default=0.5)

- **-PolarH**

  use short radii of polar hydrogens (default)

- **-NOPolarH**

  do not shorten radii of polar hydrogens

**-NOFACEhbond** do not identify HBonds to aromatic faces

**-Name** "name" specify the group name (default "dots")

- **-DOTMASTER**

  group name used as extra master={name} on lists

- **-NOGroup**

  do not generate @group statement in .kin format output

- **-KINemage**

  add @kinemage 1 statement to top of .kin format output

- **-Countdots**

  produce a count of dots-not a dotlist

- **-Unformated**

  output raw dot info

-

  name:pat:type:srcAtom:targAtom:mingap:gap:spX: spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval:

- **-OFORMAT**

  output dot info formatted for display in O

- **-XVFORMAT**

  output dot info formatted for display in XtalView

- **-ONELINE**

  output one line :contacts:by:severity:type:

- **-GAPcolor**

  color dots by gap amount (default)

- **-ATOMcolor**

  color dots by atom type

- **-BASEcolor**

  color dots by nucleic acid base type

- **-COLORBase**

  color dots by gap and nucleic acid base type

**-OUTCOLor** "name" specify the point color for **-OUT** (default "gray")

- **-GAPWeight**#

  set weight for scoring gaps (default 0.25)

**-BUMPWeight**# set relative scale for scoring bumps (default 10.0)

- **-HBWeight**#

  set relative scale for scoring Hbonds (default 4.0)

- **-DIVLow**#.#

  Division for Bump categories    (default **-0**.4)

- **-DIVHigh**#.#

  Division for Contact categories (default  0.25)

- **-MINOCCupancy**#.#

  Occupancy below this is same as zero (default  0.02)

- **-ELEMent**

  add master buttons for different elements in kin output

- **-NOHBOUT**

  do not output contacts for HBonds

- **-NOCLASHOUT**

  do not output contacts for clashes

- **-NOVDWOUT**

  do not output contacts for van der Waals interactions

- **-ONLYBADOUT**

  onlybadout output bad clashes (severe overlap contacts)

- **-SUMMARY**

  output summary list of contacts and clashes

- **-ONELINE**

  output summary list on oneline

- **-NOTICKs**

  do not display the residue name ticker during processing

- **-STDBONDs**

  assume only standard bonding patterns in standard residues

- **-NOPARENT**

  do not bond hydrogens based on table of parent heavy atoms

- **-SEGID**

  use the PDB SegID field to descriminate between residues

- **-OLDU**

  generate old style **-u** output: kissEdge2BullsEye, etc

- **-VErbose**

  verbose mode (default)

- **-REFerence**

  display reference string

- **-CHANGEs**

  display a list of program changes

- **-Quiet**

  quiet mode

- **-Help**

  show expanded help notice (includes other flags)

- **-VERSION**

  one line version to stdout

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

- FILE#

  within file #

- MODEL#

  within model #

- CHAINaa

  within chain a

- SEGaaaa

  segment identifier aaaa (where \_ represents blank)

- ALTa

  alternate conformation a

- ATOMaaaa

  atom name aaaa (where \_ represents blank) (all 4 characters are used so H would be ATOM\_H\_\_)

- RESaaa

  residue aaa

- \#

  residue #

- \#a

  residue #, insert a

- \#-#

  residue range # (insert codes ignored)

- a

  residue type by one letter codes   (eg. y)

- aaa

  residue type by three letter codes (eg. tyr)

-

  ALL,PROTEIN,MC,SC,BASE,ALPHA,BETA,NITROGEN,CARBON, OXYGEN,SULFUR,PHOSPHORUS,HYDROGEN,METAL,POLAR, NONPOLAR,CHARGED,DONOR,ACCEPTOR,AROMATIC,METHYL, HET,WATER,DNA,RNA

-

  all or a subset of the atoms

- OLT#

  Occupancy less than # (integer percent)

- OGT#

  Occupancy greater than # (integer percent)

- BLT#

  B-value less than # (integer)

- BGT#

  B-value greater than # (integer)

- INSa

  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

- ATOM

  1  CB  TYR    61      34.219  17.937   4.659  1.00  0.00

- bondrot:chi1:78.7:

  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

- TRANS:

  id:currpos:start:end:stepSz:x1:y1:z1:x2:y2:z2

- NULL

  \# dummy

- Bias functions:

  COS:scale:phaseOffset:frequency POLY:scale:offset:polynomialDegree CONST:value

- Branching:

  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