Index

Symbols

-assignCCP4 writedict command line option -autoMTZ aligngrid command line option flynn command line option -autoMTZ <true or false> rotfit command line option -autoThenManualSearch flynn command line option -blobsThenBox flynn command line option -blobTanimoto flynn command line option -box <filename> flynn command line option -boxpad <number> flynn command line option -chainid <chainid> flynn command line option -ciftype flynn command line option -clamp_at_level rscc command line option -densityAsIs flynn command line option -distance <value> flynn command line option -ewindow flynn command line option -Fc <columnname> aligngrid command line option flynn command line option rotfit command line option -Fdelwt <columnname> aligngrid command line option flynn command line option rotfit command line option -fit command line option -fitexit command line option -fix_serial_numbers flynn command line option -fixup_pepflips <true or false> rotfit command line option -fixup_rotamers <true or false> rotfit command line option -fixup_shapefit_residues <true or false> rotfit command line option -flatten rscc command line option -flipper flynn command line option -Fobs <columnname> aligngrid command line option flynn command line option rotfit command line option -forceExistingResidueNames writedict command line option -fragment flynn command line option -Fwt <columnname> aligngrid command line option flynn command line option rotfit command line option -grid aligngrid command line option -in <filename> flynn command line option writedict command line option -in <molecule file> rscc command line option -in <proteinfile> rotfit command line option -includeRotors writedict command line option -ligandAsIs flynn command line option -load <filename> command line option -lookup writedict command line option -manualSearch <filename> flynn command line option -map <filename> flynn command line option -map <mtz file> rotfit command line option -minimum_rscc <number> rotfit command line option -minimum_rscc_increase <number> rotfit command line option -mmff94s flynn command line option

-mtype aligngrid command line option flynn command line option -mtype <setting> rotfit command line option -mtz <mtz file> rscc command line option -out aligngrid command line option -out <filename prefix> writedict command line option -out <filename> flynn command line option -out <protein> rotfit command line option -outprot aligngrid command line option -overlays flynn command line option -padding aligngrid command line option -param <parameter filename> flynn command line option rotfit command line option -Phic <columnname> aligngrid command line option flynn command line option rotfit command line option -Phidelwt <columnname> aligngrid command line option flynn command line option rotfit command line option -Phiwt <columnname> aligngrid command line option flynn command line option rotfit command line option -planarAniline writedict command line option -precheck flynn command line option -prefix <file prefix> flynn command line option -prefix <filename prefix> writedict command line option -prot <filename> flynn command line option -protein aligngrid command line option -reportfile <filename> flynn command line option -reporthtml flynn command line option -residues flynn command line option -resname <name> flynn command line option -rms flynn command line option -rsr rscc command line option -scale aligngrid command line option -scatter rscc command line option -sortAllChiral <true/false> flynn command line option -sortBy flynn command line option -split flynn command line option -strict writedict command line option -suppressH flynn command line option writedict command line option -target aligngrid command line option -type writedict command line option -verbose aligngrid command line option flynn command line option rscc command line option writedict command line option -verbose <true or false> rotfit command line option -writeFullDict writedict command line option 1B0F 2D, [1] 3D Scene

A

active active molecule aligngrid command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ -grid -mtype -out -outprot -padding -protein -scale -target -verbose

aniline APPNAME_OE_ARCH, [1]

B

basic overview

C

CIF command line option -fit -fitexit -load <filename> connection table

covalent covalent bond

D

dictionary

E

edit	environment variable APPNAME_OE_ARCH, [1] OE_ARCH, [1], [2], [3], [4], [5], [6], [7] OE_LICENSE PATH, [1], [2], [3], [4], [5], [6], [7]

F

fitting algorithm

flynn command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ -autoThenManualSearch -blobTanimoto -blobsThenBox -box <filename> -boxpad <number> -chainid <chainid> -ciftype -densityAsIs -distance <value> -ewindow -fix_serial_numbers -flipper -fragment -in <filename> -ligandAsIs -manualSearch <filename> -map <filename> -mmff94s -mtype -out <filename> -overlays -param <parameter filename> -precheck -prefix <file prefix> -prot <filename> -reportfile <filename> -reporthtml -residues -resname <name> -rms -sortAllChiral <true/false> -sortBy -split -suppressH -verbose

G

Graphics

L

LIG	ligand fitting

M

MMFF MMFF94

MMFF94s

O

OE_ARCH, [1], [2], [3], [4], [5], [6], [7]

OE_LICENSE

P

PATH, [1], [2], [3], [4], [5], [6], [7] PHENIX

planar aniline PRO

R

refinement dictionary REFMAC5, [1] Residue

Residue Lookup rotfit command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ <true or false> -fixup_pepflips <true or false> -fixup_rotamers <true or false> -fixup_shapefit_residues <true or false> -in <proteinfile> -map <mtz file> -minimum_rscc <number> -minimum_rscc_increase <number> -mtype <setting> -out <protein> -param <parameter filename> -verbose <true or false> rscc command line option -clamp_at_level -flatten -in <molecule file> -mtz <mtz file> -rsr -scatter -verbose

S

SEI Seperating Ligands From Proteins sketcher

smiles SZYBKI

U

UNL

W

wizard workflow

writedict command line option -assignCCP4 -forceExistingResidueNames -in <filename> -includeRotors -lookup -out <filename prefix> -planarAniline -prefix <filename prefix> -strict -suppressH -type -verbose -writeFullDict