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angle_scripts.txt
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# scripts to run the code to obtain angles, run in pymol
##############################################################################
# SARS CoV 2 SL5
##############################################################################
pymol ../models/auto-drrafter_erraser/SARS-CoV-2/icSHAPE/*pdb
color grey, resid 159-182 or resid 263-282
color blue, resid 183-227
color orange, resid 228-252
color red, resid 253-262
select res1, resid 183-252 # a-b
select res2, resid 159-182 or resid 253-282 # stem-c
select ref2, (resid 182 or resid 253) and backbone # stem side
select ref1, (resid 183 or resid 252) and backbone
select end2a, resid 159-164 or resid 277-282 # stem
select end2b, resid 256-259 # c
select end1a, resid 238-243 # b
select end1b, resid 200-205 # a
run get_all_angles.py
##############################################################################
# SARS CoV 2 SL5 CASP - R1149
##############################################################################
pymol ../models/CASP/R1149/*pdb
color grey, resid 1-24 or resid 105-124
color blue, resid 25-69
color orange, resid 70-94
color red, resid 95-104
select res1, resid 25-94 # a-b
select res2, resid 1-24 or resid 95-124 # stem-c
select ref2, (resid 24 or resid 95) and backbone # stem side
select ref1, (resid 25 or resid 94) and backbone
select end2a, resid 1-6 or resid 119-124 # stem
select end2b, resid 98-101 # c
select end1a, resid 80-85 # b
select end1b, resid 42-47 # a
run get_all_angles.py
##############################################################################
# SARS CoV 1 SL5
##############################################################################
pymol ../models/auto-drrafter_erraser/SARS-CoV-1/*/*pdb
color grey, resid 150-181 or resid 262-292
color blue, resid 182-226
color orange, resid 227-251
color red, resid 252-261
select res1, resid 182-251 # a-b
select res2, resid 158-181 or resid 252-281 # stem-c
select ref2, (resid 181 or resid 252) and backbone # stem side
select ref1, (resid 182 or resid 251) and backbone
select end2a, resid 158-163 or resid 276-281 # stem
select end2b, resid 255-258 # c
select end1a, resid 237-242 # b
select end1b, resid 199-204 # a
run get_all_angles.py
##############################################################################
# MERS SL5
##############################################################################
pymol ../models/auto-drrafter_erraser/MERS/conf1/*/*.pdb
pymol ../models/auto-drrafter_erraser/MERS/conf2/*/*.pdb
pymol ../models/auto-drrafter_erraser/MERS/conf3/*/*.pdb
color grey, resid 205-227 or resid 321-339
color blue, resid 228-272
color orange, resid 273-299
color red, resid 300-320
# a only to junction
select res1, resid 228-231 or resid 264-299 # a-b
select res2, resid 205-227 or resid 300-339 # stem-c
select ref2, (resid 227 or resid 300) and backbone # stem side
select ref1, (resid 228 or resid 299) and backbone
select end2a, resid 205-210 or resid 231-339 # stem
select end2b, resid 307-313 # c
select end1a, resid 287-292 # b
select end1b, resid 231 or resid 264-268 # a
run get_all_angles.py
select res1, resid 228-231 or resid 264-299 # a-b to internal loop
select res2, resid 232-263 # a-b from internal loop change
select ref1, (resid 227 or resid 300) and backbone # stem side
select ref2, (resid 228 or resid 299) and backbone
select end1b, resid 213 or resid 246-250 # internal loop
select end2b, resid 246-251 # a
select end1a, resid 287-292 # b
select end1b, resid 213 or resid 246-250 # internal loop
run get_all_angles.py
##############################################################################
# BtCoV-HKU5 SL5
##############################################################################
pymol ../models/auto-drrafter_erraser/BtCoV-HKU5/conf1/{icSHAPE,libraryDMS,librarySHAPE}/*.pdb
pymol ../models/auto-drrafter_erraser/BtCoV-HKU5/conf2/{icSHAPE,libraryDMS,librarySHAPE}/*.pdb
pymol ../models/auto-drrafter_erraser/BtCoV-HKU5/conf3/{icSHAPE,libraryDMS,librarySHAPE}/*.pdb
pymol ../models/auto-drrafter_erraser/BtCoV-HKU5/conf4/{icSHAPE,librarySHAPE}/*.pdb
color grey, resid 187-209 or resid 303-321
color blue, resid 210-254
color orange, resid 255-281
color red, resid 282-302
# a only to junction
select res1, resid 210-213 or resid 246-281 # a-b
select res2, resid 187-209 or resid 282-321 # stem-c
select ref2, (resid 209 or resid 282) and backbone # stem side
select ref1, (resid 210 or resid 281) and backbone
select end2a, resid 187-192 or resid 216-321 # stem
select end2b, resid 289-295 # c
select end1a, resid 269-274 # b
select end1b, resid 213 or resid 246-250 # a
run get_all_angles.py
select res1, resid 210-213 or resid 246-281 # a-b to internal loop
select res2, resid 214-245 # a-b from internal loop
select ref1, (resid 209 or resid 282) and backbone # stem side
select ref2, (resid 210 or resid 281) and backbone
select end2a, resid 213 or resid 246-250 # internal loop
select end2b, resid 228-233 # a
select end1a, resid 269-274 # b
select end1b, resid 213 or resid 246-250 # internal loop
run get_all_angles.py
##############################################################################
# BtCoV-HKU5 SL5 CASP - R1156
##############################################################################
pymol ../models/CASP/R1156/*pdb
color grey, resid 1-23 or resid 117-135
color blue, resid 24-68
color orange, resid 69-95
color red, resid 96-116
# a only to junction
select res1, resid 24-27 or resid 60-95 # a-b
select res2, resid 1-23 or resid 96-135 # stem-c
select ref2, (resid 23 or resid 96) and backbone # stem side
select ref1, (resid 24 or resid 95) and backbone
select end2a, resid 1-192 or resid 30-135 # stem
select end2b, resid 103-109 # c
select end1a, resid 83-88 # b
select end1b, resid 27 or resid 60-64 # a
run get_all_angles.py
select res1, resid 24-27 or resid 60-95 # a-b to internal loop
select res2, resid 28-59 # a-b from internal loop
select ref1, (resid 23 or resid 96) and backbone # stem side
select ref2, (resid 24 or resid 95) and backbone
select end2a, resid 27 or resid 60-64 # internal loop
select end2b, resid 42-47 # a
select end1a, resid 83-88 # b
select end1b, resid 27 or resid 60-64 # internal loop
run get_all_angles.py
##############################################################################
# HCoV-229E
##############################################################################
pymol ../models/auto-drrafter_erraser/HCoV-229E/manual/*.pdb
color grey, resid 153-167 or resid 280-292
color blue, resid 168-221
color orange, resid 222-248
color red, resid 250-279
color black, resid 249
select res1, resid 168-248 # a-b
select res2, resid 153-167 or resid 250-292 # stem-c
select ref2, (resid 167 or resid 250) and backbone # stem side
select ref1, (resid 168 or resid 248) and backbone
select end2a, resid 153-158 or resid 287-292 # stem
select end2b, resid 262-267 # c
select end1a, resid 233-238 # b
select end1b, resid 192-197 # a
run get_all_angles.py
# nl63 --> can only estimate based on map