Prime User Manual - ISP

sequences
coloring....................................................... 14
command menu for....................................... 8
cropping...................................................... 18
editing......................................................... 10
exporting....................................................... 9
maximum length................................... 18, 25
multiple....................................................... 18
names.................................................... 18, 23
non-unique.................................................. 18
selecting...................................................... 18
standard code.............................................. 18
unusable...................................................... 23
Set Template Regions........................................ 13
color scheme............................................... 36
Set Template Regions toolbar button ................ 36
side chains......................................................... 36
optimizing................................................... 37
predicting.................................................... 36
rotamers ...................................................... 37
unfreezing in loop refinement..................... 66
similarity, BLOSUM62 matrix ......................... 23
Slide As Block ............................................ 13, 33
Slide Freely ................................................. 13, 33
solvation............................................................ 40
sorting tables, by column heading ................ 8, 22
SSA ................................................................. 136
SSP profile, in Fold Recognition ...................... 43
SSpro................................................... 29, 44, 121
SSPs ................................................................ 136
command menu for....................................... 8
composite.................................................... 33
deleting ................................................... 8, 31
editing......................................................... 13
exporting........................................... 8, 30, 43
in Fold Recognition .................................... 43
hiding all....................................................... 8
importing .............................................. 30, 43
retrieving unmodified ........................... 31, 46
in Sequence Viewer ...................................... 8
standard residues............................................... 51
Step View ............................................................ 8
steps
action ............................................................ 8
available and unavailable.............................. 9
Find Homologs ..................................... 17, 18
Input Sequence ........................................... 17
Index
name ............................................................. 8
panel layout .................................................. 7
structalign utility.................................... 115
structurally aligned templates ........................... 23
structure refinement, loop ................................. 51
structures
coloring....................................................... 14
structures, exporting........................................ 115
Surface Generalized Born (SGB)...................... 40
T
tables ................................................................... 8
cells............................................................. 22
sorting........................................................... 8
in Step View.................................................. 8
of templates ................................................ 47
Template ID color scheme ................................ 11
template sequence ........................................... 136
templates
multiple....................................................... 36
regions ........................................................ 36
structurally aligned ..................................... 23
Templates table ................................................. 47
third-party programs ......................... 44, 121, 122
Threading ........................................................ 136
Threading path ............................................ 17, 25
tilde symbol, for unlocked gap.................... 14, 33
Title, PDB header.............................................. 23
toolbar, Prime................................................ 8, 13
tooltips .......................................................... 8, 22
for buttons................................................... 13
for table entries............................................. 8
truncated-Newton.............................................. 62
U
unlocking gaps ............................................ 14, 33
unusable sequence............................................. 23
Update (button) ................................................. 33
utilities
getpdb...................................................... 22
seqconvert .............................. 30, 43, 116
structalign........................................ 115
V
V (Visualization) column.................................. 49
View SSA.......................................................... 14
Prime 2.5 User Manual 141