Other structure programs Insight II Swiss PDB-Viewer QUANTA/CHARMm and Quanta 2005 for proteins SYBYL with FUGUE and FlexX for drugs O or FRODO for x-ray MolMol for NMR PovChem, Rasmol, CHARMm

Ranges Zones give the residue range: 17 or but not only P than you can pick a range in the graphic window

PROT All proteins WATER All waters DRUG All drugs, ligands, ions NUC All nucleic acids SUG All sugars ALL All residues HELIX All helical residues STRAND All strand residues (-SHEET takes same ranges) ION All ions OXT All C-terminal oxygens All residues of a certain type Start with – (minus sign) to remove things from selection. I.e. TOT –SUG gives everything except sugars. Ranges

Numbering You can number directly a residue for example 27 in 3ERA the LYS (or with O27 if you need the number in brackets) but if LYS is not in m1 but in m3 you can number it as S2 27 or as U2 27. Try the numbering with LISTA

WHAT IF> getmol 1boy Do you mean: /g/data9/data/pdb/1boy.brk Y/N ? y Give the set-name (1boy.brk) : THR THR ASN THR VAL ALA ALA TYR ASN LEU THR TRP LYS SER THR ASN PHE LYS THR ILE LEU GLU TRP GLU PRO LYS PRO VAL ASN GLN VAL TYR THR VAL GLN ILE SER THR LYS SER GLY ASP TRP LYS SER LYS CYS PHE TYR THR THR ASP THR GLU CYS ASP LEU THR ASP GLU ILE VAL LYS ASP VAL LYS GLN THR TYR LEU ALA ARG VAL PHE SER TYR PRO ALA GLY ASN VAL GLU SER THR GLY SER ALA GLY GLU PRO LEU TYR GLU ASN SER PRO GLU PHE THR PRO TYR LEU GLU THR ASN LEU GLY GLN PRO THR WHAT IF> %shosou Content of the SOUP. See the writeup for an explanation. Molecule Range Type Set name 1 1 ( 3) 211 ( 213) Protein SET_1boy.brk ( 213) 212 ( 213) E O2 <- 211 SET_1boy.brk ( HOH ) 213 ( HOH ) water ( 110) SET_1boy.brk WHAT IF>

Three letter codes for menue The following three letter codes are associated with entire menus. ACC Has to do with ACCessibility BFT B-FacTor BLD BuiLD (mainly protein) CHK CHecK CHI Torsion angle CLU CLUster of 3D related residues COL COLour DG Distance Geometry rotamer and loop search DIG Digitalization (reconstruction from stereo plots) FAM FAMily, range of covalently connected residues GRA GRAphics GRI GRIn and GRId GRO GROmos H2O Water HBO Hydrogen BOnd (potential hydrogen bonds) HB2 Hydrogen Bond 2nd version (optimal hydrogen bonds) HSP HSsP (multiple sequence alignment files) HST Helix, Strand, Turn (in other words: secondary structure) LAB LABel (not picked label, but label in MOL-item) MAP 3D electron density, property or probability distribution MAP NEU NEUral net NMR Nuclear Magnetic Resonanced

3 letters: DEL, INI, ON/OFF, TAB,ROW GRA,SHO but DG pairs of options: GET/MAK, SAV/RES exceptions: SIMPLE DIRECT Three-letter codes for options

The correspondence between numbers and colours is: 1 Blue 30 Blue-ish purple 60 Purple 90 Red-ish purple 120 Red 150 Orange 180 Yellow 190 Light brown 220 Soft green 240 Green 270 Funny green 300 White-ish green 330 Light blue 360 Blue Also you can type: RED, GREEN, YELLOW, BLUE,PURPLE, ORANGE, CYAN, MAGENTA. LAST COLOUR COUNTS Colours