/usr/share/doc/garlic-doc/commands/pla.html is in garlic-doc 1.6-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 | <html>
<head>
<title>
PLA, PLANE
</title>
</head>
<h1 align=center>
PLA, PLANE
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
PLA, PLANE - manipulate the plane associated with the structure.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
PLA
<br>
PLA RAD value
<br>
PLA TRA value
<br>
PLA OFF
<br>
PLANE
<br>
PLANE RADIUS value
<br>
PLANE TRANSPARENCY value
<br>
PLANE OFF
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
When a PDB file is read, a new structure is stored into program memory.
A single plane is associated with this structure. By default, the plane is
invisible and movement controls are affecting both the structure and the
associated plane. The command PLANE may be used to make the plane visible,
to set the plane transparency or radius, or to hide the plane.
<br><br>
Plane is represented by an ellipse. One side of this ellipse will be colored
blue and other side will be colored orange-red. Blue side is treated as top
(upper) side, while orange-red side is treated as bottom side. Far side of
the plane is dark.
<br><br>
The transparency value should be between 0 and 1. If the transparency is equal
to zero the plane is opaque. Default plane transparency is 0.4 (hard-coded).
The initial (default) plane radius is based on the spacial extent of the
structure. The image below shows two semi-transparent planes: the left plane
is seen from above, while the right plane is seen from below. The transparency
is equal to 0.3 for both planes.
<br><br>
<img src="plane1.jpg">
<br><br>
Plane may be used for different purposes:
<br>
(1) To distinguish protein domains. Many soluble proteins fold into two
domains. Plane may be used to outline the border between these domains.
<br>
(2) Atoms may be selected according to their position with respect to plane.
The command SEL ABO (SELECT ABOVE) selects atoms which are above the plane.
The command SEL BEL (SELECT BELOW) selects atoms which are below the plane.
The image below shows what may be achieved when applying different drawing
styles to atoms on different sides of the plane.
<br>
(3) To represent the cellular membrane. Since version 1.2, garlic is capable
to represent the membrane directly, so this usage of planes is obsolete.
<br><br>
<img src="plane2.jpg">
<br><br>
<font color=#880000>
<b>
KEYWORDS
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
KEYWORD
<br>
(SHORT)
</td>
<td align="left">
KEYWORD
<br>
(LONG)
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
OFF
</td>
<td align="left">
OFF
</td>
<td align="left">
Hide plane.
</td>
<tr>
<td align="left">
RAD
</td>
<td align="left">
RADIUS
</td>
<td align="left">
Set plane radius (value should be given in angstroms).
</td>
<tr>
<td align="left">
TRA
</td>
<td align="left">
TRANSPARENCY
</td>
<td align="left">
Set plane transparency (between 0 and 1).
</td>
</table>
<br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
plane
</td>
<td align="left">
Make the plane visible.
</td>
<tr>
<td align="left">
pla rad 20
</td>
<td align="left">
Change plane radius to 20 angstroms.
</td>
<tr>
<td align="left">
pla tra 0.3
</td>
<td align="left">
Change plane transparency (new value: 0.3).
</td>
<tr>
<td align="left">
plane off
</td>
<td align="left">
Hide plane.
</td>
</table>
<br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) By default, the plane moves with the structure. If movement controls
affect only the plane, be sure to make it visible. Otherwise, you may push
the plane far away from the object to which this plane belongs.
<br><br>
(2) In garlic source code, each plane is defined by the plane center (three
coordinates) and by the normal vector (three-component vector).
<br><br>
(3) At present, garlic associates only one plane with each structure. If for
some reason you need two planes (for example, to simulate the cellular
membrane), use the following trick:
<br>
(3.1) Prepare the structure and its associated plane (the first plane).
<br>
(3.2) Load another structure (something small, like a single residue)
and hide it.
<br>
(3.3) Make the plane (which is associated with this small structure) visible.
<br>
(3.4) Change radius and transparency for the second plane.
<br>
(3.5) Set the position and orientation of this plane.
<br>
If you learn this trick, you will be able to prepare images like this one:
<br><br>
<img src="plane3.jpg">
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
LOAD is used to load the structure (PDB file). MOVE is used to define which
object should be moved. POSITION is used to place the chosen object
(structure, plane, membrane or all) to arbitrary position. SELECT ABOVE
selects atoms above the plane, while SELECT BELOW selects atoms below
the plane.
<br><br>
<hr size="3">
</html>
|