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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. Zones give the residue range: 17 or 19 20

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other structure programs
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 19 20

0

but not 17 19 20 0

only P than you can pick a range in the graphic window

Ranges
slide3

Ranges

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

<RESNAM> All residues of a certain type

Start with – (minus sign) to remove things from selection. I.e. TOT –SUG gives everything except sugars.

numbering
Numbering

You can number directly a residue

for example 27 in 3ERA the LYS

(or with O27if 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

slide5

WHAT IF> getmol 1boy

Do you mean: /g/data9/data/pdb/1boy.brk Y/N ? y

Give the set-name (1boy.brk) :

1 - 10 THR THR ASN THR VAL ALA ALA TYR ASN LEU

11 - 20 THR TRP LYS SER THR ASN PHE LYS THR ILE

21 - 30 LEU GLU TRP GLU PRO LYS PRO VAL ASN GLN

31 - 40 VAL TYR THR VAL GLN ILE SER THR LYS SER

41 - 50 GLY ASP TRP LYS SER LYS CYS PHE TYR THR

51 - 60 THR ASP THR GLU CYS ASP LEU THR ASP GLU

61 - 70 ILE VAL LYS ASP VAL LYS GLN THR TYR LEU

71 - 80 ALA ARG VAL PHE SER TYR PRO ALA GLY ASN

81 - 90 VAL GLU SER THR GLY SER ALA GLY GLU PRO

91 - 100 LEU TYR GLU ASN SER PRO GLU PHE THR PRO

101 - 110 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

2 212 ( 213) 212 ( 213) E O2 <- 211 SET_1boy.brk

3 213 ( HOH ) 213 ( HOH ) water ( 110) SET_1boy.brk

WHAT IF>

three letter codes for menue
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

slide7

Three-letter codes for options

3 letters:

DEL, INI, ON/OFF, TAB,ROW GRA,SHO

but DG

pairs of options:

GET/MAK, SAV/RES

exceptions:

SIMPLE

DIRECT

slide8

Colours

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

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