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Ticket #16469: cmds.cxc

File cmds.cxc, 8.6 KB (added by Eric Pettersen, 12 months ago)
Command recovered from damaged session file

Line
1	open /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/AF-Q8IJP3-F1-model_v4.pdb
2	open 8HFO
3	open /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/chai1_PfCTS_ligand_XG8/pred.model_idx_4.rank_1.cif /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/chai1_PfCTS_ligand_XG8/pred.model_idx_3.rank_0.cif /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/chai1_PfCTS_ligand_XG8/pred.model_idx_2.rank_3.cif /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/chai1_PfCTS_ligand_XG8/pred.model_idx_1.rank_4.cif /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/chai1_PfCTS_ligand_XG8/pred.model_idx_0.rank_2.cif
4	ui tool show Matchmaker
5	matchmaker #1,3-7 to #2
6	matchmaker #1,4 to #2 showAlignment true
7	matchmaker #4 to #1 showAlignment true
8	ui tool show "Renumber Residues"
9	renumber #3/A #4/A #5/A #6/A #7/A seqStart 91
10	hide #7 models
11	hide #6 models
12	hide #5 models
13	hide #3 models
14	select add #2
15	select subtract #2
16	select add #2
17	select subtract #2
18	select add #2
19	mlp sel
20	select subtract #2
21	hide #2.2 models
22	select add #4
23	color bfactor sel
24	hide #2.1 models
25	hide #!2 models
26	hide #1 models
27	mlp sel
28	show #1 models
29	select subtract #4/A:518@CD2
30	select subtract #4/A:514@CG2
31	select subtract #4/A:454@CD2
32	select subtract #4/A:459@CD1
33	select up
34	select down
35	select down
36	select up
37	select down
38	select clear
39	select #4/A:454@CD2
40	select add #4/A:514@CG2
41	select add #4/A:518@CD2
42	select up
43	select add #4/A:449@CG2
44	select up
45	select add #4/A:446@CD1
46	select up
47	select add #4/A:452@CE2
48	select up
49	show sel atoms
50	hide #!4 models
51	show #!4 models
52	hide #1 models
53	show sel atoms
54	hide #4.1 models
55	show #1 models
56	show #4.1 models
57	info residues sel
58	hide #4.1 models
59	hide #1 models
60	color sel byhetero
61	color (#!4 & sel) byhetero
62	label (#!4 & sel) text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
63	info residues sel
64	show #4.1 models
65	hide #4.1 models
66	show #5 models
67	show #6 models
68	show #7 models
69	hide #7 models
70	hide #6 models
71	hide #5 models
72	hide #4.2 models
73	select #4/A:457
74	select add #4/A:514@CG1
75	select up
76	select up
77	select #4/A:452@CZ
78	select add #4/A:454@CD2
79	info atoms sel
80	info atomattr
81	select #4/A:452@CZs
82	select #4/A:452@CZ
83	info atoms sel
84	info atoms sel attribute bfactor
85	info atoms sel attribute bfactor
86	select clear
87	select #4/A:454@CD2
88	info atoms sel attribute bfactor
89	show #4.1 models
90	show #1 models
91	hide #4.1 models
92	show #2.2 models
93	hide #2.2 models
94	show #4.1 models
95	show #7 models
96	select add #7
97	ui tool show "Renumber Residues"
98	renumber #7/A seqStart 1
99	hide #4.1 models
100	hide #!4 models
101	hide #!2 models
102	hide #1 models
103	hide #7 models
104	select subtract #7
105	show #4.1 models
106	hide #4.1 models
107	show #7 models
108	hide #!4 models
109	select add #7
110	select subtract #7
111	hide #7 models
112	show #!4 models
113	show #4.1 models
114	hide #4.1 models
115	hide #!4 models
116	show #!4 models
117	show #4.1 models
118	hide #4.1 models
119	show #4.1 models
120	select #4/A:168@CE1
121	select add #4/A:332@CD1
122	select add #4/A:213@CD2
123	select add #4/A:212@CD1
124	select add #4/A:217@CD1
125	select up
126	select add #4/A:203@CD1
127	select up
128	select add #4/A:223@OH
129	select up
130	select add #4/A:160@CG2
131	select up
132	select add #4/A:361@CZ
133	select up
134	select subtract #4/A:223@OH
135	select subtract #4/A:223@CZ
136	select subtract #4/A:223@CE2
137	select subtract #4/A:223@CD1
138	select subtract #4/A:223@CE1
139	select subtract #4/A:223@CD2
140	select subtract #4/A:223@CA
141	select up
142	select down
143	select subtract #4/A:212@CD1
144	select subtract #4/A:212@CD2
145	select subtract #4/A:212@CB
146	select subtract #4/A:212@CA
147	select subtract #4/A:212@N
148	select subtract #4/A:213@O
149	select subtract #4/A:213@CA
150	select subtract #4/A:213@N
151	select subtract #4/A:160@CG1
152	select subtract #4/A:160@CG2
153	select add #4/A:160@CG2
154	select subtract #4/A:160@CG2
155	select subtract #4/A:160@CB
156	select subtract #4/A:160@O
157	select up
158	select down
159	select down
160	select up
161	select down
162	select up
163	select down
164	select down
165	select down
166	select up
167	select add #4/A:362@CE1
168	select up
169	select subtract #4/A:160@CG2
170	select subtract #4/A:160@CG1
171	select add #4/A:157@CA
172	select subtract #4/A:160@O
173	select subtract #4/A:157@CA
174	select subtract #4/A:160@CB
175	select up
176	select down
177	select subtract #4/A:212@CD2
178	select up
179	select down
180	select down
181	select subtract #4/A:212@CD1
182	select up
183	select subtract #4/A:160@CG1
184	select subtract #4/A:160@CG2
185	select subtract #4/A:160@O
186	select add #4/A:160@CG2
187	select up
188	show sel atoms
189	hide #4.1 models
190	select subtract #4/A:160@CB
191	select #4/A:160
192	undo
193	select subtract #4/A:160
194	select subtract #4/A:361
195	select subtract #4/A:362
196	select subtract #4/A:212
197	select subtract #4/A:168
198	select add #4/A:168
199	show #4.1 models
200	hide #4.1 models
201	select add #4/A:361
202	show #4.1 models
203	hide #4.1 models
204	show #4.1 models
205	hide #4.1 models
206	show #4.1 models
207	hide #4.1 models
208	info atoms sel
209	info residues sel
210	show #4.1 models
211	save /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS.cxs
212	hide #4.1 models
213	show #4.1 models
214	hide #4.1 models
215	show #4.1 models
216	select add #4
217	select subtract #4
218	select add #4.1
219	mlp sel
220	select subtract #4.1
221	show #1 models
222	show #2.2 models
223	hide #4.1 models
224	hide #1 models
225	hide #!2 models
226	show #!2 models
227	show #2.1 models
228	hide #2.1 models
229	hide #!4 models
230	hide #!2 models
231	show #!2 models
232	show #2.1 models
233	hide #2.2 models
234	hide #2.1 models
235	hide #!2 models
236	show #!4 models
237	show #!2 models
238	hide #!4 models
239	show #!4 models
240	show #1 models
241	hide #!4 models
242	hide #!2 models
243	show #3 models
244	hide #1 models
245	show #4.2 models
246	show #6 models
247	show #7 models
248	show #5 models
249	hide #7 models
250	show #1 models
251	select #2/A:10
252	select #2/A:10-16 #4/A:99-104
253	select #2/A:0
254	select #2/A:0-2 #4/A:91-92
255	select #1/A:89
256	select #1/A:89-91 #4/A:91
257	select #1/A:94
258	select #1/A:94-96 #4/A:94-96
259	select #1/A:92
260	select #1/A:92-95 #4/A:92-95
261	select #1/A:91
262	select #1/A:91-95 #4/A:91-95
263	select #4/A:472
264	select #2/A:356-412 #4/A:472-535
265	hide #1 models
266	select #5/A:422
267	hide #6 models
268	hide #5 models
269	hide #4.2 models
270	select add #5
271	show #4.2 models
272	select subtract #5
273	hide #3 models
274	hide #4.2 models
275	show #4.2 models
276	select #4/A:423
277	select #4/A:422
278	select #4/A:422-427
279	select #4/A:422
280	select #4/A:422-535
281	select #4/A:91
282	select #4/A:91-425
283	select #4/A:91
284	select #4/A:91-419
285	select #4/A:91-421
286	select #4/A:91
287	select #4/A:91-415
288	select #4/A:146
289	select #4/A:398
290	select #4/A:375
291	select #4/A:375
292	select #4/A:91-375
293	show #!2 models
294	hide #!2 models
295	hide #!4 models
296	select add #4
297	select subtract #4
298	hide #4.2 models
299	show #7 models
300	show #6 models
301	hide #7 models
302	show #5 models
303	show #3 models
304	hide #5 models
305	hide #6 models
306	mlp #3
307	show #2.2 models
308	hide #!3 models
309	hide #2.2 models
310	hide #!2 models
311	show #1 models
312	show #!2 models
313	hide #!2 models
314	hide #1 models
315	show #1 models
316	show #!2 models
317	show #!3 models
318	hide #!2 models
319	hide #1 models
320	select #3:91-375
321	save /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS_nterm_chai1.pdb models #3 selectedOnly true
322	hide #!3 models
323	select add #3
324	show #!2 models
325	open /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS_nterm_chai1.pdb
326	select add #8
327	color bfactor sel & #8
328	show #1 models
329	show #7 models
330	hide #7 models
331	show #2.2 models
332	hide #2.2 models
333	show #4.1 models
334	hide #4.1 models
335	hide #!4 models
336	select subtract #3.1
337	select add #3
338	show #!3 models
339	hide #1 models
340	show #1 models
341	hide #!2 models
342	show #!2 models
343	hide #!2 models
344	show #!2 models
345	hide #3.1 models
346	show #3.1 models
347	hide #3.1 models
348	hide #!3 models
349	select subtract #3.1
350	select add #3
351	select subtract #3.1
352	select add #3
353	select subtract #3
354	hide #1 models
355	mlp sel
356	hide #!2 models
357	select #8/A:143@CD2
358	select add #8/A:209@CD1
359	select up
360	select add #8/A:154@CD1
361	select up
362	select add #8/A:158@CD1
363	select up
364	select add #8/A:162@CE1
365	select up
366	show #!2 models
367	hide #!2 models
368	select add #8/A:155@CD1
369	select up
370	select add #8/A:163@CZ
371	select up
372	select add #8/A:159@CD1
373	select up
374	select add #8/A:120@CE1
375	select up
376	select add #8/A:372@CD2
377	select up
378	select add #8/A:150@CG2
379	select up
380	select add #8/A:107@CD1
381	select up
382	show sel atoms
383	color (#!8 & sel) byelement
384	hide #8.1 models
385	label (#!8 & sel) text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
386	show #8.1 models
387	mlp sel
388	hide #8.1 models
389	select subtract #8/A:162
390	select add #8/A:162
391	select subtract #8/A:162
392	info residues sel
393	swapaa #8:107,120,143,150,154,155,158,159,163,209,372 seq:A
394	close #8.1
395	select add #8
396	mlp sel
397	select #8/A:339@CD1
398	select add #8/A:128@CD1
399	select up
400	swapaa #8:128,339 seq:A
401	close #8.1
402	select add #8
403	mlp sel
404	show #!2 models
405	hide #!2 models
406	show #!2 models
407	hide #8.2 models
408	hide #8.1 models
409	select subtract #8.2
410	select subtract #8.1
411	select add #8
412	save /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS_nterm_mut_chai1.pdb models #8 selectedOnly true
413	close #8
414	open /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS_nterm_chai1.pdb /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS_nterm_mut_chai1.pdb
415	save /Users/iphan/Documents/ssgcid/SVTD_18_SDDC_minibinders/PfCTS/PfCTS.cxs

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