Sophie

Sophie

distrib > Mandriva > cooker > i586 > by-pkgid > eede1088262777189a3d3f16cb3dc560 > files > 267

garlic-1.6-6.i586.rpm

<html>

<head>
<title>
Garlic Reference Card, Version 1.6
</title>
</head>

<table border=1 cellspacing=0 cellpading=0>

<td align="left">
<b>
COM.
</b>
</td>

<td align="left">
<b>
ARGUMENTS
</b>
</td>

<td align="left">
<b>
APPLIES TO
</b>
</td>

<td align="left">
<b>
DESCRIPTION
</b>
</td>

<tr>

<td align="left">
ADD
</td>

<td align="left">
the same as for SEL
</td>

<td align="left">
selection
</td>

<td align="left">
Add to selection
</td>

<tr>

<td align="left">
ANG
</td>

<td align="left">
angle (degrees)
</td>

<td align="left">
helical wheel,
<br>
hydrophob. mom.
</td>

<td align="left">
Angle for helical wheel
<br>
and hydrophobic moment
<br>
calculation
</td>

<tr>

<td align="left">
ATO
</td>

<td align="left">
0, 1, 2, 3, 4, 5, 6, 7, BAL, BA2, SMA,
<br>
SM2, COV, CO2, SPA, SP2, BIG, BI2
</td>

<td align="left">
selection
</td>

<td align="left">
Set drawing style for atoms
</td>

<tr>

<td align="left">
BAC
</td>

<td align="left">
0, 1, 2, 3, 4, 5, OFF
</td>

<td align="left">
selection
</td>

<td align="left">
Draw backbone
</td>

<tr>

<td align="left">
BAL
</td>

<td align="left">
radius (angstroms)
</td>

<td align="left">
structure
</td>

<td align="left">
Set ball radius
</td>

<tr>

<td align="left">
BG
</td>

<td align="left">
color_specification
</td>

<td align="left">
main window
</td>

<td align="left">
Change background color
</td>

<tr>

<td align="left">
BLU
</td>

<td align="left">
width height, OFF
</td>

<td align="left">
main window
</td>

<td align="left">
Blur (soften) image
</td>

<tr>

<td align="left">
BON
</td>

<td align="left">
0, 1, 2, 3, 4, 5, NICE,
<br>
REFRESH
</td>

<td align="left">
selection
</td>

<td align="left">
Set bond style or
<br>
refresh (reset) bonds
</td>

<tr>

<td align="left">
CAT
</td>

<td align="left">
structure_identifier
</td>

<td align="left">
structure
</td>

<td align="left">
Catch structure
</td>

<tr>

<td align="left">
CEN
</td>

<td align="left">
none
</td>

<td align="left">
structure, selection
</td>

<td align="left">
Redefine system origin
</td>

<tr>

<td align="left">
COL
</td>

<td align="left">
detailed_color_specification,
<br>
red, green, blue, yellow, cyan,
<br>
magenta, white, yellow-green,
<br>
cyan-green, cyan-blue, magenta-blue,
<br>
magenta-red, orange, cold (default),
<br>
hot, monochrome, cpk, size, zebra,
<br>
chain, hyphob, weighted
</td>

<td align="left">
selection
</td>

<td align="left">
Assign color;
<br>
do not abbreviate
<br>
color scheme name!
</td>

<tr>

<td align="left">
COM
</td>

<td align="left">
none, OFF,
<br>
minimal_score segment_width,
<br>
CORNER serial1 serial2,
<br>
ZOOM zoom_factor
</td>

<td align="left">
both sequence
<br>
buffers
</td>

<td align="left">
Compare two sequences
</td>

<tr>

<td align="left">
CRE
</td>

<td align="left">
none
</td>

<td align="left">
main seq. buffer,
<br>
main struct. buffer
</td>

<td align="left">
Create new structure
</td>

<tr>

<td align="left">
DIS
</td>

<td align="left">
structure_identifier
<br>
*, all
</td>

<td align="left">
structure
</td>

<td align="left">
Discard structure
</td>

<tr>

<td align="left">
DOC
</td>

<td align="left">
identifier_1 identifier_2
<br>
OFF
</td>

<td align="left">
Two structures
</td>

<td align="left">
Prepare two structures
<br>
for docking
</td>

<tr>

<td align="left">
DUM
</td>

<td align="left">
AVE filename,
<br>
HYD filename,
<br>
F1 ... F7 (with filename)
</td>

<td align="left">
Hydrophobicity functions
</td>

<td align="left">
Dump numeric values for
<br>
selected hydrophob. f.
</td>

<tr>

<td align="left">
EDI
</td>

<td align="left">
OFF, ATO, BON atom1 atom2, CLI,
<br>
DIM, MAI, OME, PHI, PSI, SID 
</td>

<td align="left">
structure
</td>

<td align="left">
Edit structure
</td>

<tr>

<td align="left">
EXE
</td>

<td align="left">
file_name
</td>

<td align="left">
script file
</td>

<td align="left">
Execute script
</td>

<tr>

<td align="left">
EXI
</td>

<td align="left">
none
</td>

<td align="left">
garlic session
</td>

<td align="left">
Quit garlic session
</td>

<tr>

<td align="left">
FAD
</td>

<td align="left">
FRO shift, BAC shift, OFF, PLA,
<br>
SPH, CYL, HALF-SPH, HALF-CYL
</td>

<td align="left">
structure
</td>

<td align="left">
Change color fading
</td>

<tr>

<td align="left">
FG
</td>

<td align="left">
color_specification
</td>

<td align="left">
main window
</td>

<td align="left">
Change text color
</td>

<tr>

<td align="left">
FON
</td>

<td align="left">
font_name
</td>

<td align="left">
all windows
</td>

<td align="left">
Change font
</td>

<tr>

<td align="left">
GRO
</td>

<td align="left">
id1 id2 ... idN,
<br>
ALL, SAV filename, SSC filename
</td>

<td align="left">
structure(s)
</td>

<td align="left">
Group structures
</td>

<tr>

<td align="left">
HID
</td>

<td align="left">
none
</td>

<td align="left">
selection
</td>

<td align="left">
Hide atoms and bonds
</td>

<tr>

<td align="left">
HYB
</td>

<td align="left">
none, OFF
</td>

<td align="left">
structure
</td>

<td align="left">
Generate hydrogen bonds
</td>

<tr>

<td align="left">
LAB
</td>

<td align="left">
none, OFF
</td>

<td align="left">
selection
</td>

<td align="left">
Show labels
</td>

<tr>

<td align="left">
LOA
</td>

<td align="left">
file_name
</td>

<td align="left">
structure_file
</td>

<td align="left">
Load structure (file)
</td>

<tr>

<td align="left">
LOG
</td>

<td align="left">
file_name, OFF
</td>

<td align="left">
commands
</td>

<td align="left">
Log garlic commands
</td>

<tr>

<td align="left">
MEM
</td>

<td align="left">
none, OFF, BET, RAD radius,
<br>
THI thickness, TRA transparency
</td>

<td align="left">
membrane
</td>

<td align="left">
Show or hide membrane,
<br>
set properties
</td>

<tr>

<td align="left">
MON
</td>

<td align="left">
none
</td>

<td align="left">
main window
</td>

<td align="left">
Switch to mono mode
</td>

<tr>

<td align="left">
MOV
</td>

<td align="left">
ALL, MEM, PLA, STR
</td>

<td align="left">
struct., memb., plane
</td>

<td align="left">
Attach controls to object 
</td>

<tr>

<td align="left">
NEI
</td>

<td align="left">
none, VER, OFF
</td>

<td align="left">
main window
</td>

<td align="left">
Show or hide
<br>
sequence neighborhood
</td>

<tr>

<td align="left">
PAT
</td>

<td align="left">
= res_name_list1 / * / res_name_list2 ...
<br>
TOL number_allowed_errors
</td>

<td align="left">
pattern buffer
</td>

<td align="left">
define sequence pattern
<br>
or set pattern tolerance
</td>

<tr>

<td align="left">
PAU
</td>

<td align="left">
none
</td>

<td align="left">
garlic script
</td>

<td align="left">
Pause script execution
</td>

<tr>

<td align="left">
PLA
</td>

<td align="left">
none, OFF, RAD radius,
<br>
TRA transparency
</td>

<td align="left">
plane
</td>

<td align="left">
Show or hide plane,
<br>
set properties
</td>

<tr>

<td align="left">
PLO
</td>

<td align="left">
HYD, MOM, OFF,
<br>
HYD start_residue end_residue,
<br>
MOM_start_residue end_residue
<br>
SID start_residue end_residue
<br>
F1, F2, F3, F4, F5, F6, F7
</td>
<td align="left">

sequence buffer

</td>
<td align="left">
Plot average hydrophob.,
<br>
hydrophobic moment,
<br>
sided hydrophobicity
<br>
or some other function
</td>

<tr>

<td align="left">
POS
</td>
  
<td align="left">
x, y, z
</td>

<td align="left">
structure
</td>

<td align="left">
Move to (x, y, z)
</td>

<tr>

<td align="left">
PRO
</td>

<td align="left">
radius (angstroms)
</td>

<td align="left">
structure
</td>

<td align="left">
Set probe radius
</td>

<tr>

<td align="left">
QUI
</td>

<td align="left">
none
</td>

<td align="left">
garlic session
</td>

<td align="left">
Quit garlic session
</td>

<tr>

<td align="left">
RAD
</td>

<td align="left">
radius (angstroms)
</td>

<td align="left">
Selection sphere
</td>

<td align="left">
Change sel. sphere radius
</td>

<tr>

<td align="left">
RAM
</td>

<td align="left">
none, SEL, OFF
</td>

<td align="left">
structure
</td>

<td align="left">
Draw Ramachandran plot
</td>

<tr>

<td align="left">
REF
</td>

<td align="left">
none, OFF
</td>

<td align="left">
main window
</td>

<td align="left">
Refreshing on/off
</td>

<tr>

<td align="left">
REG
</td>

<td align="left">
none
</td>

<td align="left">
mail
</td>

<td align="left">
Register garlic
</td>

<tr>

<td align="left">
REP
</td>

<td align="left">
none
</td>

<td align="left">
structure, seq. buffer
</td>

<td align="left">
Replace selected residues
</td>

<tr>

<td align="left">
RES
</td>

<td align="left">
the same as for SEL
</td>

<td align="left">
selection
</td>

<td align="left">
Restrict selection
</td>

<tr>

<td align="left">
ROT
</td>

<td align="left">
axis angle (degrees)
</td>

<td align="left">
structure
</td>

<td align="left">
Rotate
</td>

<tr>

<td align="left">
SAV
</td>

<td align="left">
file_name
<br>
file_name SEL
</td>

<td align="left">
structure, selection
</td>

<td align="left">
Save atomic data to file
<br>
(SEL = selection only)
</td>

<tr>

<td align="left">
SCA
</td>

<td align="left">
EIS, KD, INT, IN2, OCT, DIF
</td>

<td align="left">
hydrophobicity scale
</td>

<td align="left">
Choose hydrophob. scale:
<br>
Eisenberg, Kyte-Doolittle,
<br>
interface, octanol
</td>

<tr>

<td align="left">
SEL
</td>

<td align="left">
chains/res_nums/res_names/atom_names,
<br>
residue_numbers,
<br>
residue_names,
<br>
*, ALL, ABO, ACI, ALI, ALT, BAD, BAS,
<br>
BEL, CHA, CIS, COM, HET, PHO, MAI,
<br>
MOD model_number, NEG, PAT, POL, POS,
<br>
SEQ, SID, SMA, SPH, TIN, TM, TRA, TRI,
<br>
2C3, 2CZ3, 2NZ3, 3C4, 3CZ4, 3NZ4, 3C5,
<br>
3CZ5, 3NZ5, 4C5, 4CZ5, 4NZ5, 3C6, 3CZ6,
<br>
3NZ6, 4C6, 4CZ6, 4NZ6, 5C6, 5CZ6, 5NZ6,
<br>
4C7, 4CZ7, 4NZ7, 5C7, 5CZ7, 5NZ7, 5P7,
<br>
6P7, 4C9, 4CZ9, 4NZ9, 5C9, 5CZ9, 5NZ9
</td>

<td align="left">
structure,
<br>
selection
</td>

<td align="left">
Define new selection
<br>
(overwrite previous);
<br>
C = charged,
<br>
Z = zwitterionic,
<br>
N = negative,
<br>
P = polar
</td>

<tr>

<td align="left">
SEQ
</td>

<td align="left">
= three_letters_code, LOAD filename,
<br>
FROM structure_identifier, COPY,
<br>
SAVE filename, SWN filename, RESET
</td>

<td align="left">
sequence buffer,
<br>
reference seq. buffer
</td>

<td align="left">
Manipulate sequence
<br>
buffer
</td>

<tr>

<td align="left">
SET
</td>

<td align="left">
PHI, PSI, OME, CHI1, CHI2, CHI3,
<br>
CHI4, CHI5 (angle required, degrees)
</td>

<td align="left">
structure
</td>

<td align="left">
Set dihedral angle
</td>

<tr>

<td align="left">
SHO
</td>

<td align="left">
none
</td>

<td align="left">
selection
</td>

<td align="left">
Show atoms and bonds
</td>

<tr>

<td align="left">
SLA
</td>

<td align="left">
FRO shift, BAC shift, OFF, PLA,
<br>
SPH, CYL, HALF-SPH, HALF-CYL
</td>

<td align="left">
structure
</td>

<td align="left">
Change slab
</td>

<tr>

<td align="left">
SSB
</td>

<td align="left">
0, 1, 2, 3, 4, 5, NICE
</td>

<td align="left">
disulfide bonds
</td>

<td align="left">
Style for disulf. bonds
</td>

<tr>

<td align="left">
STE
</td>

<td align="left">
none, OFF
</td>

<td align="left">
main window
</td>

<td align="left">
Switch to stereo mode
</td>

<tr>

<td align="left">
STI
</td>

<td align="left">
radius (angstroms)
</td>

<td align="left">
structure
</td>

<td align="left">
Set stick radius
</td>

<tr>

<td align="left">
STR
</td>

<td align="left">
= one_letter_code, LOAD filename,
<br>
FROM structure_identifier, COPY,
<br>
SAVE filename, RESET
</td>

<td align="left">
sec. struct. buffer,
<br>
ref. sec. struct. buffer
</td>

<td align="left">
Manipulate secondary
<br>
structure buffer
</td>

<tr>

<td align="left">
TAG
</td>

<td align="left">
"string", OFF
</td>

<td align="left">
structure
</td>

<td align="left">
Assign or remove tag
</td>

<tr>

<td align="left">
TBG
</td>

<td align="left">
color_specification
</td>

<td align="left">
input and output win.
</td>

<td align="left">
Change text background
</td>

<tr>

<td align="left">
TFG
</td>

<td align="left">
color_specification
</td>

<td align="left">
input and output win.
</td>

<td align="left">
Change text color
</td>

<tr>

<td align="left">
TIT
</td>

<td align="left">
identifier x y "string"
<br>
identifier x y
<br>
identifier OFF
</td>

<td align="left">
main window
</td>

<td align="left">
Add, move or
<br>
remove title
</td>

<tr>

<td align="left">
TRA
</td>

<td align="left">
axis shift
</td>

<td align="left">
structure
</td>

<td align="left">
Translate
</td>

<tr>

<td align="left">
VEN
</td>

<td align="left">
none, OFF,
<br>
start_residue end_residue
</td>

<td align="left">
sequence buffer
</td>

<td align="left">
Draw Venn diagram with
<br>
statistics
</td>

<tr>

<td align="left">
WHE
</td>

<td align="left">
none, OFF, CLOCKWISE,
<br>
start_index end_index,
<br>
start_index end_index CLOCKWISE
</td>

<td align="left">
sequence buffer
</td>

<td align="left">
Draw helical wheel
</td>

<tr>

<td align="left">
WIN
</td>

<td align="left">
number_of_residues
</td>

<td align="left">
sliding window
</td>

<td align="left">
Set sliding window width
</td>

</table>

</html>

Perl :: Catalyst :: PostgreSQL :: RPM Valid HTML 4.01 Transitional