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PROGRAM:

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

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