KING-PROBE(1)

💖 NAME 💖

king-probe — evaluate and visualize protein interatomic packing. that's literally the whole job bestie, and it does it gorgeously ✨

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✨ DESCRIPTION ✨

okay so here's the tea ☕ the syntax is literally this:

probe input.pdb >> out.kin

or, when you're feeling fancy and want to go full main character:

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

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🎀 Flags 🎀

• -SElf — self intersection: src -> src (this is the default, periodt)
• -Both — intersect both ways: src <=> targ
• -ONce — single intersection: src -> targ
• -OUt — external van der Waals surface of src (the solvent contact surface)
• -AUTObondrot filename — read and process an autobondrot file

shortcuts, bestie:

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

• -DEFAULTs — same as <<NO FLAGS>>, except it lets some other flags through too
• -SCSurface — same as: -drop -rad1.4 -out "not water"
• -EXPOsed — same as: -drop -rad1.4 -out (note: you supply the pattern yourself, diva)
• -ASurface — same as: -drop -rad0.0 -add1.4 -out "not water"
• -ACCESS — same as: -drop -rad0.0 -add1.4 -out (note: user supplies the 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

heads up bestie: BOTH and ONCE need two patterns, while OUT, SELF and DUMPATOMINFO need just one pattern. that's the rule 🙈

• -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

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🌸 Pattern elements 🌸

(these should be put in quotes on the command line, ok bestie? 🎀)

• 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)

also these, as a set:

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

which means 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

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so the way patterns work: you can combine them into comma separated lists, like "trp,phe,tyr" which means TRP or PHE or TYR. iconic.

patterns that are separated by blanks must all be true, like "chainb 1-5" meaning residues 1 to 5 in chain B. no cap.

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. obsessed with the flexibility honestly.

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an autobondrot file is similar to other PDB input files, except it also includes info identifying atoms subject to rotations and other transformations 🦋

here's an example autobondrot file fragment showing a 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 💜

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🧚 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)

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Set orientation: GO:angle1:angle2:...

Include files: @filename

Comments: # comment text

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and just so we're clear, the program signs itself off like this: probe: version 2.13.110909, Copyright 1996-2011, J. Michael Word

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okay that's the whole page bestie, you ate that 💅✨ this was king-probe version 2.13.110909-1, dated September 2015 — now go pack some atoms, you icon 👑💖