king-probe1

Evaluate and visualize protein interatomic packing

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13