-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtutorial_channel_raw.html
282 lines (275 loc) · 12.8 KB
/
tutorial_channel_raw.html
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
<p class="tutorial_text">The Phenix video tutorials explain how to run Phenix
programs and how to interpret the results. All tutorial videos are
available on the Phenix tutorials YouTube channel: <a class="reference external" href="https://www.youtube.com/c/phenixtutorials">www.youtube.com/c/phenixtutorials</a>.</p>
<p>A list of all videos is also below (click on the panels to expand the view).</p>
<div class="tutorial_container">
<button class="tutorial_accordion tutorial_color1">
<table style="width:100%">
<tr>
<td style="width: 15%"><img style="width: 90px;height: 84px;padding-right:10px;" src="../images/cryoem_clear.png" alt="cryoem image"></td>
<td>Tools for Cryo-EM</td>
</tr>
</table>
</button>
<div class="tutorial_panel">
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Overview</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_cryoem.jpg" alt="cryoem image" ></td>
<td><a class="reference external" href="https://youtu.be/GL6FtZRzoQs">Overview of cryo-EM tools in Phenix</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Map-tools</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_autosharpen.png" ></td>
<td><a class="reference external" href="https://youtu.be/S56rYoZWxnM">Automated map sharpening with phenix.autosharpen</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_resolve_em.jpg" ></td>
<td><a class="reference external" href="https://youtu.be/4axYwCn2VWI">Density modification for cryo-EM maps</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_map_model.png" ></td>
<td><a class="reference external" href="https://youtu.be/ZYcG8dlmc18">Automatic map interpretation with map_to_model</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Refinement</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_realspace.jpg" alt="phenix.real_space_refine"></td>
<td><a class="reference external" href="https://youtu.be/shmBHtyUdCc">How to run real_space_refine</a></td>
</tr>
</table>
</div>
</div>
<div class="tutorial_container">
<button class="tutorial_accordion tutorial_color2">
<table style="width:100%">
<tr>
<td style="width: 15%"><img style="width: 90px;height: 87px;padding-right:10px;" src="../images/xray.png" alt="xray image"></td>
<td>Tools for X-ray crystallography</td>
</tr>
</table>
</button>
<div class="tutorial_panel">
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Reflection data</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_plan_SAD.jpg"></td>
<td><a class="reference external" href="https://youtu.be/w8sl_BEwuEU">Simulate a SAD experiment with phenix.plan_sad_experiment</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_scale_merge.png"></td>
<td><a class="reference external" href="https://youtu.be/j-mZGA5uLb0">Scaling and merging anomalous data</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Data analysis</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_xtriage.png" alt="xtriage image" ></td>
<td><a class="reference external" href="https://youtu.be/lWBDjfVN9D4">Checking data quality with phenix.xtriage</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_xtriage2.png" alt="xtriage2 image" ></td>
<td><a class="reference external" href="https://youtu.be/7QbPvVA-wRQ">Advanced Tutorial Xtriage - translational NCS (tNCS)</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_xtriage3.png" alt="xtriage3 image" ></td>
<td><a class="reference external" href="https://youtu.be/36mc80lrSVU">Advanced Tutorial Xtriage - Checking for twinning</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_xtriage4.png" alt="xtriage4 image" ></td>
<td><a class="reference external" href="https://youtu.be/QlWahDGBTbE">Advanced Tutorial Xtriage - Space Group Identification, Ice rings & Wilson Plot</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC;text-align: center; padding:2px">Molecular replacement</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_phaser.jpg"></td>
<td><a class="reference external" href="https://youtu.be/lJ7t8dgfFjk">How to run Phaser-MR</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Experimental Phasing</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_autosol.jpg"></td>
<td><a class="reference external" href="https://youtu.be/_Olb8_hYn4U">SAD phasing using AutoSol</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Model Building</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_autobuild.jpg" alt="phenix.refine"></td>
<td><a class="reference external" href="https://youtu.be/og3TM9Cwve0">Automated model building with Phenix AutoBuild</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Refinement</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_refine.jpg" alt="phenix.refine"></td>
<td><a class="reference external" href="https://youtu.be/6m9dX8gA5o0">How to run phenix.refine</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Other tools</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_structure_comparison.jpg"></td>
<td><a class="reference external" href="https://youtu.be/lrCLzJGR6Y0">How to run Structure Comparison</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_ligandfit.jpg"></td>
<td><a class="reference external" href="https://youtu.be/hLr4owC1pTA">Fitting ligands into density with phenix.ligandfit</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_polder.jpg"></td>
<td><a class="reference external" href="https://youtu.be/TcTuMJayh5c">Calculating polder maps</a></td>
</tr>
</table>
</div>
</div>
<div class="tutorial_container">
<button class="tutorial_accordion tutorial_color3">
<table style="width:100%">
<tr>
<td style="width: 15%"><img style="width: 90px;height: 102px;padding-right:10px;" src="../images/aa.png" alt="aa image"></td>
<td>Other tutorials (apply to both cryo-EM and Xtallography)</td>
</tr>
</table>
</button>
<div class="tutorial_panel">
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Ligands</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_elbow.jpg" alt="elbow"></td>
<td><a class="reference external" href="https://youtu.be/8qVYTUVKlbQ">Basic Phenix eLBOW tutorial</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Validation</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_molprobity.jpg"></td>
<td><a class="reference external" href="https://youtu.be/VMfHGfQpQ8s">How to run MolProbity - step by step (web interface and Phenix GUI)</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_molprobity_aac.jpg"></td>
<td><a class="reference external" href="https://youtu.be/5ceIMxKbB-A">MolProbity: All atom contacts tutorial</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Mixed Tools</h3>
<table>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_mult_strategies.jpg" ></td>
<td><a class="reference external" href="https://youtu.be/sQeTcs4kM4k">How to use multiple refinement strategies and apply them to selected parts of a model</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_ss_restraints.jpg" ></td>
<td><a class="reference external" href="https://youtu.be/9dCkAdR1RDk">How to use secondary structure restraints</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_pdbtools.jpg" ></td>
<td><a class="reference external" href="https://youtu.be/uJs6ah27PKE">How to run PDB tools</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_change_parameters.jpg"></td>
<td><a class="reference external" href="https://youtu.be/qB8W_6yuw5k">Changing custom parameters in phenix.refine</a></td>
</tr>
<tr>
<td><img style="width:96px;height:54px;" src="../images/thumbnail_selection_syntax.jpg"></td>
<td><a class="reference external" href="https://youtu.be/K28q378F39s">Explaining the atom selection syntax</a></td>
</tr>
</table>
</div>
</div>
<div class="tutorial_container">
<button class="tutorial_accordion tutorial_color4">
<table style="width:100%">
<tr>
<td style="width: 15%"><img style="width: 100px;height: 62px;padding-right:10px;" src="../images/chalkboard.png" alt="aa image"></td>
<td>Lectures</td>
</tr>
</table>
</button>
<div class="tutorial_panel">
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Mini-lectures</h3>
<table>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/_BK2ETHuZhU">Mini-lecture: Density modification</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Other</h3>
<table>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/limaUsNAVL8">Introduction to interactive low-resolution model building with ISOLDE</a></td>
</tr>
</table>
<h3 style="background-color: #DCDCDC; text-align: center; padding:2px">Full length lectures (45 min - 1 hour)</h3>
<table>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/dqYWj6CxuUQ">SBGrid: Density Modification and Model Building with cryo-EM maps (T. Terwilliger)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/pfSMMGoEQtU">SBGrid: Atomic model refinement and validation in Phenix (P. Afonine)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/muhW7F67-6U">SBGrid: Map Sharpening; Model Building; other cryo-EM tools in Phenix (D. Liebschner)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/T3fiMcXgKuU">CCP4 Study weekend 2020: Cryo-EM map density modification and model-building (T. Terwilliger)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/BQl8nxBnHPE">CCP4 Study weekend 2020; EM Model Refinement (D. Liebschner)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/-AvxsjbNQqw">SBGrid: Atomic model, map and model-to-map fit validation (P. Afonine)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/akk8Q17gRgg">Experimental Phasing (T. Terwilliger)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/lYh69KT4zI4">Molecular Replacement in Phenix (P. Adams)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/bkKKwQ7pHac">Structure Refinement in Phenix (P. Afonine)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/wQEYZ6SXK4M">Structure Validation with Phenix (P. Adams)</a></td>
</tr>
<tr>
<td></td>
<td><a class="reference external" href="https://youtu.be/nQDB6Tu_Quo">Model-building using cryo-EM and crystallographic maps (T. Terwilliger)</a></td>
</tr>
<tr>
<td></td>
<td></td>
</tr>
</table>
</div>
</div>
<script>
var acc = document.getElementsByClassName("tutorial_accordion");
var i;
for (i = 0; i < acc.length; i++) {
acc[i].addEventListener("click", function() {
this.classList.toggle("active");
var panel = this.nextElementSibling;
if (panel.style.maxHeight){
panel.style.maxHeight = null;
} else {
panel.style.maxHeight = panel.scrollHeight + "px";
}
});
}
</script>