Prime User Manual - ISP

Symbols
+ (plus sign), in Pfam sequence ........................ 21
- (hyphen)
for locked gap ....................................... 14, 33
for loop ........................................... 13, 31, 46
~ (tilde), for unlocked gap........................... 14, 33
A
Add Anchors ............................................... 14, 33
Align program................................................... 47
aligned regions .................................................. 36
alignment......................................................... 135
editing................................................... 13, 33
alignment score ................................................. 34
interpretation of values ............................... 71
alpha carbons
aligning structures by ............................... 119
constraining specific ................................. 100
maximum movement .......................... 65, 101
anchors ............................................................ 135
alignment constraints............................ 14, 33
removing............................................... 14, 33
setting ................................................... 14, 33
ASL................................................................. 135
atom names, correcting ..................................... 54
ATOM records ................................................ 125
B
Balloon Help ....................................................... 8
binding sites, aligning ....................................... 74
bit score............................................................. 23
BLAST
database format......................................... 123
expectation value ........................................ 23
percentage gaps .......................................... 23
updating database ..................................... 120
BLAST/PSI-BLAST....................................... 121
blocks, sliding ............................................. 13, 33
BLOSUM62 similarity matrix .......................... 23
bond orders, assigning ...................................... 53
bonds, to metals ................................................ 52
Build Structure step........................................... 35
C
chain lengths ..................................................... 18
Index
chain name ........................................................ 23
chains, multiple......................................... 18, 102
charged residues................................................ 33
code, sequence .................................................. 18
cofactors.............................................. 36, 37, 135
Color by Sequence ............................................ 10
Color Scheme.............................................. 10, 14
Prime Display Menu................................... 10
Prime toolbar .............................................. 10
color schemes.............................................. 10–11
for Set Template Regions ........................... 36
columns
sorting............................................... 8, 22, 48
V (Visualization) ........................................ 49
Comparative Modeling ............................... 1, 135
Comparative Modeling Path ................... 9, 17, 25
composite SSP .................................................. 33
composite templates........................................ 135
Compound (PDB COMPND) ........................... 23
conserved residues ...................................... 36, 47
constraints ....................................................... 135
alpha carbon.............................................. 100
atom pair..................................................... 99
continuum solvation model............................... 40
conventions, document...................................... ix
cooperative refinement of loops........................ 60
coordinate copying............................................ 36
Covalent Docking panel.................................... 78
covalently bound ligands .................................. 51
crystal symmetry............................................... 64
C-terminal gaps........................................... 13, 33
D
Delete
Prime runs..................................................... 6
SSP ......................................................... 8, 31
deletions .............................................. 36, 51, 135
directory
installation .................................................... 3
Maestro working........................................... 3
Display menu (Prime)................................. 10, 13
domains....................................................... 18, 25
E
E (for beta strand) ................................. 13, 31, 46
Edit menu (Prime)............................................. 13
Prime 2.5 User Manual 137