Prime User Manual - ISP

138
Index
Edit SSP ............................................................ 13
editing alignment .............................................. 33
editing sequences .............................................. 10
EMBL ............................................................... 18
Energy Analysis task......................................... 58
energy minimization ......................................... 62
entries, Project Table......................................... 16
environment variables ..................................... 123
SCHRODINGER .............................................. 3
SCHRODINGER_PDB...................................... 3
error messages................................... 18, 127, 129
Expect column .................................................. 23
expectation value............................................... 23
Export Sequences............................................ 8, 9
Export SSP.............................................. 8, 30, 43
extracting sequence names................................ 18
F
family ................................................................ 21
FASTA
file format ............................................. 18, 30
file header ................................................... 18
file formats ........................................................ 18
File menu ............................................................ 6
Job Options................................................. 14
Find Homologs step .................................... 17, 18
Fold Recognition....................................... 43, 135
folds................................................................... 47
Font Size, in Sequence Viewer ......................... 12
force field
Build Structure............................................ 40
energy minimization................................... 62
nonstandard residues .................................. 52
single-point energy ..................................... 58
formal charges, correcting ................................ 53
G
gaps ................................................................. 135
C-terminal............................................. 13, 33
locking .................................................. 14, 33
N-terminal............................................. 13, 33
percentage................................................... 23
in query....................................................... 23
in secondary structure......................... 34, 129
in template .................................................. 23
unlocking .............................................. 14, 33
Prime 2.5 User Manual
GENBANK ....................................................... 18
getpdb utility.................................................. 22
GPCRs
aligning....................................................... 31
SSPs for ...................................................... 29
Guide......................................................... 8, 9, 13
H
H (for alpha helix)................................. 13, 31, 46
header
FASTA file.................................................. 18
PDB ............................................................ 18
helix, building ................................................. 101
HETATMs ....................................................... 135
HETATOMs .................................................... 135
hidden sequences .............................................. 21
Hide All (SSPs)................................................... 8
HMMER/Pfam.................................... 21, 28, 121
homologs......................................................... 135
importing .................................................... 19
Homologs table ................................................. 23
host machine ..................................................... 14
hydrogens, adding............................................. 52
hydrophobic residues ........................................ 33
hyphen symbol
for locked gap ....................................... 14, 33
for loop ........................................... 13, 31, 46
I
ID, PDB chain................................................... 23
Identities column............................................... 23
Import SSP.................................................. 30, 43
importing structurally aligned templates .......... 19
Include ligands and cofactors window.............. 37
Input Sequence step .......................................... 17
insertions....................................... 33, 36, 51, 135
J
Job Monitor panel ....................................... 15, 38
job options......................................................... 14
Job Options dialog box ................................. 9, 14
job status icon ............................................... 8, 15
jobs
killing.......................................................... 15
monitoring .................................................. 15
stopping ...................................................... 38