/usr/share/doc/garlic-doc/commands/ram.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 | <html>
<head>
<title>
RAM, RAMACHANDRAN
</title>
</head>
<h1 align=center>
RAM, RAMACHANDRAN
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
RAM, RAMACHANDRAN - draw Ramachandran plot.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
RAM
<br>
RAM SEL
<br>
RAM OFF
<br>
RAMACHANDRAN
<br>
RAMACHANDRAN SEL
<br>
RAMACHANDRAN OFF
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
Draw Ramachandran plot (only for proteins). The main chain torsion angles,
phi and psi, are used to prepare two-dimensional scatter plot. Residues
for which both phi and psi angle may be calculated will be shown as small
circles. The horizontal axis (abscisa) is used for phi values, while the
vertical axis (ordinate) is used for psi values. Blue color is used for trans
residues, magenta for cis residues and red for bad residues. Trans residues
are drawn first, followed by cis residues. Bad residues are drawn last.
A residue is treated as bad if peptide unit associated with this residue is
not planar. Peptide unit is considered as non-planar if it is twisted for
more than 20 degrees. Terminal residues will be missing, because at least one
of dihedral angles is not defined for such residues.
<br><br>
<font color=#880000>
<b>
DIHEDRAL ANGLES
<br>
</b>
</font>
Click
<a href="dihedrals.html">
here
</a> for definitions of dihedral angles.
<br><br>
<font color=#880000>
<b>
KEYWORDS
<br>
</b>
</font>
If used without any keyword, the command RAM will prepare the Ramachandran
plot for protein structure(s) which are currently being handled ("caught").
Keyword OFF is used to switch off the Ramachandran plot, i.e. to return to
the main drawing mode (atomic structure display). If keyword SEL (SELECTED)
is used, only the residues which are currently selected will be visible in
the Ramachandran plot. A residue is treated as selected if the first atom of
this residue is selected. For proteins, this is usually N (nitrogen) atom.
Here is the overview:
<br><br>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
KEYWORD
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
ram sel
</td>
<td align="left">
Draw Ramachandran plot for selected residues.
</td>
<tr>
<td align="left">
ram off
</td>
<td align="left">
Return to default drawing mode (atomic structure).
<br>
Instead using this command, you can hit the ESCAPE key.
</td>
</table>
<br>
<font color=#880000>
<b>
MOUSE USAGE
<br>
</b>
</font>
Pointing device (mouse) may be used to identify individual residues in
Ramachandran plot. Just place the mouse pointer above the selected residue
and the most important data for this residue will be shown in the output
window. The output window will look like this:
<br><br>
<img src="ramacont.gif">
<br><br>
<font color=#880000>
<b>
EXAMPLE OF RAMACHANDRAN PLOT
<br>
</b>
</font>
The example below show the Ramachandran plot for photosynthetic reaction center
from Rhodopseudomonas viridis.
<br><br>
<img src="ramaplot.gif">
<br><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">
ram
</td>
<td align="left">
Draw Ramachandran plot for all residues.
</td>
<tr>
<td align="left">
ram off
</td>
<td align="left">
Return to default drawing mode (atomic structure).
</td>
<tr>
<td align="left">
ram sel
</td>
<td align="left">
Draw Ramachandran plot for selected residues.
</td>
<tr>
<td align="left">
sel pro
<br>
ram sel
</td>
<td align="left">
Select all prolines and draw Ramachandran
<br>
plot for prolines.
</td>
<tr>
<td align="left">
sel cis
<br>
ram sel
</td>
<td align="left">
Select all residues in cis conformation and
<br>
draw Ramachandran plot for them.
</td>
<tr>
<td align="left">
sel bad
<br>
ram sel
</td>
<td align="left">
Select bad residues (peptide unit not planar)
<br>
and draw Ramachandran plot.
</td>
<tr>
<td align="left">
sel tra
<br>
ram sel
</td>
<td align="left">
Select all residues in trans conformation and
<br>
draw Ramachandran plot.
</td>
</table>
<br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) Instead using the command RAMA OFF, the ESCAPE key may be pressed to
return to the main drawing mode.
<br><br>
(2) G. N. Ramachandran devised in the late 1960's the steric constraints for
amino acid residues in proteins. As the number of high resolution structures
is increasing, it appears evident that these old constrains are becoming
obsolete. If you are interested in this problem, read this article:
<br><br>
<a href="http://xray.bmc.uu.se/~gerard/rama/ramarev.html">
http://xray.bmc.uu.se/~gerard/rama/ramarev.html
</a>
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
SEL may be used to select a portion of protein structure, to reduce the
amount of data in Ramachandran plot.
<br><br>
<hr size="3">
</html>
|