Changes between Initial Version and Version 1 of Ticket #18030


Ignore:
Timestamp:
Jun 20, 2025, 9:45:15 AM (4 months ago)
Author:
pett
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18030

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #18030 – Description

    initial v1  
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    3740 > color sel #7a2634ff
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    3832 > color sel #752532ff
    3833 
    3834 > color sel #722431ff
    3835 
    3836 [Repeated 1 time(s)]
    3837 
    3838 > color sel #732431ff
    3839 
    3840 > color sel #742431ff
    3841 
    3842 > select up
    3843 
    3844 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    3845 
    3846 > select down
    3847 
    3848 1455 atoms, 1487 bonds, 175 residues, 1 model selected 
    3849 
    3850 > select up
    3851 
    3852 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    3853 
    3854 > select up
    3855 
    3856 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    3857 
    3858 > select down
    3859 
    3860 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    3861 
    3862 > select up
    3863 
    3864 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    3865 
    3866 > select up
    3867 
    3868 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    3869 
    3870 > select down
    3871 
    3872 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    3873 
    3874 > select up
    3875 
    3876 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    3877 
    3878 > select down
    3879 
    3880 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    3881 
    3882 > select up
    3883 
    3884 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    3885 
    3886 > select clear
    3887 
    3888 > select add #8
    3889 
    3890 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    3891 
    3892 > select subtract #8
    3893 
    3894 Nothing selected 
    3895 
    3896 > select add #8
    3897 
    3898 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    3899 
    3900 > color #8 #bb3b50ff
    3901 
    3902 > color #8 #c1153cff
    3903 
    3904 > color #8 #bb3b50ff
    3905 
    3906 [Repeated 1 time(s)]
    3907 
    3908 > select #8/A
    3909 
    3910 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    3911 
    3912 > color (#!8 & sel) #bb3c53ff
    3913 
    3914 > color (#!8 & sel) #ba3c53ff
    3915 
    3916 > color (#!8 & sel) #b43a50ff
    3917 
    3918 > color (#!8 & sel) #b1394fff
    3919 
    3920 > color (#!8 & sel) #b0384eff
    3921 
    3922 > color (#!8 & sel) #a8364bff
    3923 
    3924 > color (#!8 & sel) #942f42ff
    3925 
    3926 > color (#!8 & sel) #8e2e3fff
    3927 
    3928 > color (#!8 & sel) #8b2d3dff
    3929 
    3930 > color (#!8 & sel) #852b3bff
    3931 
    3932 > color (#!8 & sel) #7e2938ff
    3933 
    3934 > color (#!8 & sel) #7e2838ff
    3935 
    3936 > color (#!8 & sel) #7d2837ff
    3937 
    3938 > color (#!8 & sel) #782735ff
    3939 
    3940 > color (#!8 & sel) #722533ff
    3941 
    3942 > color (#!8 & sel) #6e2331ff
    3943 
    3944 > color (#!8 & sel) #6a222fff
    3945 
    3946 > color (#!8 & sel) #69222eff
    3947 
    3948 > color (#!8 & sel) #68212eff
    3949 
    3950 > color (#!8 & sel) #65212dff
    3951 
    3952 > color (#!8 & sel) #63202cff
    3953 
    3954 > color (#!8 & sel) #62202cff
    3955 
    3956 > color (#!8 & sel) #611f2bff
    3957 
    3958 > color (#!8 & sel) #601f2bff
    3959 
    3960 > color (#!8 & sel) #601f2aff
    3961 
    3962 > color (#!8 & sel) #5f1f2aff
    3963 
    3964 [Repeated 1 time(s)]
    3965 
    3966 > color (#!8 & sel) #63202cff
    3967 
    3968 > color (#!8 & sel) #65202dff
    3969 
    3970 > color (#!8 & sel) #66212dff
    3971 
    3972 > color (#!8 & sel) #67212eff
    3973 
    3974 [Repeated 1 time(s)]
    3975 
    3976 > color (#!8 & sel) #621f2bff
    3977 
    3978 > color (#!8 & sel) #611f2bff
    3979 
    3980 > color (#!8 & sel) #601f2bff
    3981 
    3982 > color (#!8 & sel) #5e1e2aff
    3983 
    3984 > color (#!8 & sel) #5d1e29ff
    3985 
    3986 [Repeated 1 time(s)]
    3987 
    3988 > color (#!8 & sel) #5e1e2aff
    3989 
    3990 [Repeated 1 time(s)]
    3991 
    3992 > color (#!8 & sel) #601f2bff
    3993 
    3994 [Repeated 1 time(s)]
    3995 
    3996 > color (#!8 & sel) #611f2bff
    3997 
    3998 [Repeated 1 time(s)]
    3999 
    4000 > color (#!8 & sel) #621f2bff
    4001 
    4002 > color (#!8 & sel) #62202cff
    4003 
    4004 > color (#!8 & sel) #63202cff
    4005 
    4006 > color (#!8 & sel) #64202cff
    4007 
    4008 > color (#!8 & sel) #67212eff
    4009 
    4010 [Repeated 1 time(s)]
    4011 
    4012 > color (#!8 & sel) #62202cff
    4013 
    4014 > color (#!8 & sel) #601f2bff
    4015 
    4016 [Repeated 1 time(s)]
    4017 
    4018 > color (#!8 & sel) #611f2bff
    4019 
    4020 > color (#!8 & sel) #63202cff
    4021 
    4022 > show #!4 models
    4023 
    4024 Alignment identifier is 8/A 
    4025 
    4026 > select clear
    4027 
    4028 > select add #4
    4029 
    4030 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    4031 
    4032 > interfaces select & ~solvent
    4033 
    4034 Missing or invalid "atoms" argument: invalid atoms specifier 
    4035 Alignment identifier is 1 
    4036 Alignment identifier is 3 
    4037 Alignment identifier is 4/E 
    4038 Alignment identifier is 4 
    4039 Alignment identifier is 5 
    4040 Alignment identifier is 4/K 
    4041 Alignment identifier is 6 
    4042 Alignment identifier is 4/O 
    4043 
    4044 > select clear
    4045 
    4046 > select add #4
    4047 
    4048 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    4049 
    4050 > hide #!8 models
    4051 
    4052 > select #4/H-J
    4053 
    4054 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    4055 Alignment identifier is 1 
    4056 
    4057 > select #4/J:665
    4058 
    4059 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4060 
    4061 > select #4/H:673-690/J:665-668
    4062 
    4063 185 atoms, 186 bonds, 22 residues, 1 model selected 
    4064 
    4065 > show #!8 models
    4066 
    4067 > select add #8
    4068 
    4069 30200 atoms, 30865 bonds, 10 pseudobonds, 3682 residues, 3 models selected 
    4070 Alignment identifier is 2 
    4071 Alignment identifier is 3 
    4072 Alignment identifier is 8/D 
    4073 Alignment identifier is 8/E 
    4074 Alignment identifier is 4 
    4075 Alignment identifier is 5 
    4076 Alignment identifier is 8/J 
    4077 
    4078 > select #4/H:466
    4079 
    4080 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4081 
    4082 > select #4/H:466-474
    4083 
    4084 81 atoms, 80 bonds, 9 residues, 1 model selected 
    4085 
    4086 > select #4/H:465-466
    4087 
    4088 18 atoms, 17 bonds, 2 residues, 1 model selected 
    4089 
    4090 > select #4/H:465-482
    4091 
    4092 160 atoms, 160 bonds, 18 residues, 1 model selected 
    4093 
    4094 > select #4/H:483-484
    4095 
    4096 13 atoms, 12 bonds, 2 residues, 1 model selected 
    4097 
    4098 > select #4/H:483-539/I:487-539/J:490-539
    4099 
    4100 1244 atoms, 1256 bonds, 1 pseudobond, 155 residues, 2 models selected 
    4101 
    4102 > select
    4103 > #4/H:465-510,523-542,547-557,559-600,605-632,639-663,674-685/I:487-510,523-542,547-557,559-563,565-600,605-632,639-662/J:490-510,523-542,547-557,559-600,605-632,639-666
    4104 
    4105 3977 atoms, 4034 bonds, 2 pseudobonds, 473 residues, 2 models selected 
    4106 
    4107 > select clear
    4108 
    4109 > select
    4110 > #4/H:462-489,517-521,663-690/I:487-489,517-521,561-566/J:561-566,663-668
    4111 
    4112 624 atoms, 620 bonds, 2 pseudobonds, 75 residues, 2 models selected 
    4113 
    4114 > select clear
    4115 
    4116 [Repeated 1 time(s)]
    4117 
    4118 > select #4/H:465-466
    4119 
    4120 18 atoms, 17 bonds, 2 residues, 1 model selected 
    4121 
    4122 > select #4/H:465-478
    4123 
    4124 126 atoms, 126 bonds, 14 residues, 1 model selected 
    4125 
    4126 > hide #!8 models
    4127 
    4128 > select #4/H:479
    4129 
    4130 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4131 
    4132 > select #4/H:479-489/I:487-489
    4133 
    4134 113 atoms, 112 bonds, 14 residues, 1 model selected 
    4135 
    4136 > show #!8 models
    4137 
    4138 > hide #!8 models
    4139 
    4140 > select #4/H-J:490
    4141 
    4142 24 atoms, 21 bonds, 3 residues, 1 model selected 
    4143 
    4144 > select #4/H-J:490-495
    4145 
    4146 147 atoms, 144 bonds, 18 residues, 1 model selected 
    4147 
    4148 > show #!8 models
    4149 
    4150 > hide #!4 models
    4151 
    4152 > select #4/H:464-465 #8/C:464-465
    4153 
    4154 42 atoms, 42 bonds, 4 residues, 2 models selected 
    4155 
    4156 > select #4/H:464-479 #8/C:464-479
    4157 
    4158 292 atoms, 294 bonds, 32 residues, 2 models selected 
    4159 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [464-479] RMSD:
    4160 4.944 
    4161  
    4162 
    4163 > select #4/H:481 #8/C:481
    4164 
    4165 16 atoms, 14 bonds, 2 residues, 2 models selected 
    4166 
    4167 > select #4/H:481-492/J:490-492 #8/A-B:490-492/C:481-492
    4168 
    4169 261 atoms, 258 bonds, 33 residues, 2 models selected 
    4170 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [481-492] RMSD:
    4171 3.768 
    4172  
    4173 
    4174 > select #4/H,J:493 #8/A-C:493
    4175 
    4176 45 atoms, 40 bonds, 5 residues, 2 models selected 
    4177 
    4178 > select #4/H,J:493-501 #8/A-C:493-501
    4179 
    4180 370 atoms, 365 bonds, 45 residues, 2 models selected 
    4181 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [493-501] RMSD:
    4182 1.232 
    4183  
    4184 
    4185 > show #!4 models
    4186 
    4187 > hide #!4 models
    4188 
    4189 > show #!4 models
    4190 
    4191 > hide #!4 models
    4192 
    4193 > show #!4 models
    4194 
    4195 > hide #!4 models
    4196 
    4197 > show #!4 models
    4198 
    4199 > hide #!8 models
    4200 
    4201 > show #!8 models
    4202 
    4203 > hide #!4 models
    4204 
    4205 > select clear
    4206 
    4207 > show #!4 models
    4208 
    4209 > hide #!8 models
    4210 
    4211 > show #!8 models
    4212 
    4213 > hide #!4 models
    4214 
    4215 > show #!4 models
    4216 
    4217 > hide #!8 models
    4218 
    4219 > show #!8 models
    4220 
    4221 > hide #!4 models
    4222 
    4223 > show #!4 models
    4224 
    4225 > hide #!8 models
    4226 
    4227 > select #4/H:685
    4228 
    4229 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4230 
    4231 > select #4/H:677-685
    4232 
    4233 76 atoms, 75 bonds, 9 residues, 1 model selected 
    4234 
    4235 > select #4/J:666
    4236 
    4237 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4238 
    4239 > select #4/H:659-663/I:659-662/J:659-666
    4240 
    4241 150 atoms, 151 bonds, 17 residues, 1 model selected 
    4242 
    4243 > show #!8 models
    4244 
    4245 > hide #!4 models
    4246 
    4247 > select #4/J:666 #8/C:666
    4248 
    4249 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4250 
    4251 > select #4/H:659-663/J:659-666 #8/A-B:659-664/C:659-666
    4252 
    4253 287 atoms, 289 bonds, 33 residues, 2 models selected 
    4254 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [659-666] RMSD:
    4255 2.540 
    4256  
    4257 
    4258 > select #4/H:674 #8/A-C:674
    4259 
    4260 28 atoms, 24 bonds, 4 residues, 2 models selected 
    4261 
    4262 > select #4/H:674-680 #8/A-C:674-680
    4263 
    4264 248 atoms, 248 bonds, 28 residues, 2 models selected 
    4265 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [674-680] RMSD:
    4266 2.050 
    4267  
    4268 
    4269 > show #!4 models
    4270 
    4271 > hide #!8 models
    4272 
    4273 > select #4/H:674
    4274 
    4275 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4276 
    4277 > select #4/H:674-680
    4278 
    4279 62 atoms, 62 bonds, 7 residues, 1 model selected 
    4280 
    4281 > show #!8 models
    4282 
    4283 > hide #!4 models
    4284 
    4285 > select add #4
    4286 
    4287 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    4288 
    4289 > select subtract #4
    4290 
    4291 Nothing selected 
    4292 
    4293 > select #8/B
    4294 
    4295 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    4296 
    4297 > color (#!8 & sel) #63202cff
    4298 
    4299 > color (#!8 & sel) #65202dff
    4300 
    4301 > color (#!8 & sel) #66212dff
    4302 
    4303 > color (#!8 & sel) #68212eff
    4304 
    4305 > color (#!8 & sel) #69222eff
    4306 
    4307 > color (#!8 & sel) #69222fff
    4308 
    4309 [Repeated 1 time(s)]
    4310 
    4311 > color (#!8 & sel) #6b222fff
    4312 
    4313 > color (#!8 & sel) #6d2330ff
    4314 
    4315 > color (#!8 & sel) #712432ff
    4316 
    4317 > color (#!8 & sel) #762634ff
    4318 
    4319 > color (#!8 & sel) #782735ff
    4320 
    4321 > color (#!8 & sel) #7c2837ff
    4322 
    4323 > color (#!8 & sel) #832a3aff
    4324 
    4325 > color (#!8 & sel) #872b3cff
    4326 
    4327 > color (#!8 & sel) #8a2c3dff
    4328 
    4329 > color (#!8 & sel) #8d2d3fff
    4330 
    4331 > color (#!8 & sel) #922f41ff
    4332 
    4333 > color (#!8 & sel) #963043ff
    4334 
    4335 > color (#!8 & sel) #9d3346ff
    4336 
    4337 > color (#!8 & sel) #a53549ff
    4338 
    4339 > color (#!8 & sel) #ac374cff
    4340 
    4341 > color (#!8 & sel) #b33a4fff
    4342 
    4343 > color (#!8 & sel) #b73b51ff
    4344 
    4345 > color (#!8 & sel) #ba3c52ff
    4346 
    4347 > color (#!8 & sel) #bd3d54ff
    4348 
    4349 > color (#!8 & sel) #bf3d55ff
    4350 
    4351 > color (#!8 & sel) #c23e56ff
    4352 
    4353 > color (#!8 & sel) #c43f57ff
    4354 
    4355 > color (#!8 & sel) #c74058ff
    4356 
    4357 > color (#!8 & sel) #ca4159ff
    4358 
    4359 > color (#!8 & sel) #cb415aff
    4360 
    4361 > color (#!8 & sel) #ce425cff
    4362 
    4363 > color (#!8 & sel) #d0435cff
    4364 
    4365 > color (#!8 & sel) #d4445eff
    4366 
    4367 > color (#!8 & sel) #d6455fff
    4368 
    4369 [Repeated 1 time(s)]
    4370 
    4371 > color (#!8 & sel) #d7455fff
    4372 
    4373 > color (#!8 & sel) #d6455fff
    4374 
    4375 > color (#!8 & sel) #d5445fff
    4376 
    4377 > color (#!8 & sel) #d1435dff
    4378 
    4379 > color (#!8 & sel) #cf425cff
    4380 
    4381 > color (#!8 & sel) #cd425bff
    4382 
    4383 > color (#!8 & sel) #cc425bff
    4384 
    4385 > color (#!8 & sel) #ca415aff
    4386 
    4387 > select #8/A
    4388 
    4389 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    4390 
    4391 > color (#!8 & sel) #ca4159ff
    4392 
    4393 > color (#!8 & sel) #bb3c53ff
    4394 
    4395 > color (#!8 & sel) #ac374cff
    4396 
    4397 > color (#!8 & sel) #a63549ff
    4398 
    4399 > color (#!8 & sel) #9d3245ff
    4400 
    4401 > color (#!8 & sel) #8e2e3fff
    4402 
    4403 > color (#!8 & sel) #852b3bff
    4404 
    4405 > color (#!8 & sel) #7c2837ff
    4406 
    4407 > color (#!8 & sel) #752634ff
    4408 
    4409 > color (#!8 & sel) #722533ff
    4410 
    4411 > color (#!8 & sel) #6e2331ff
    4412 
    4413 > color (#!8 & sel) #69222fff
    4414 
    4415 > color (#!8 & sel) #65212dff
    4416 
    4417 > color (#!8 & sel) #621f2bff
    4418 
    4419 > color (#!8 & sel) #601f2bff
    4420 
    4421 > color (#!8 & sel) #5e1e2aff
    4422 
    4423 > color (#!8 & sel) #5d1e29ff
    4424 
    4425 > color (#!8 & sel) #5c1e29ff
    4426 
    4427 > color (#!8 & sel) #5b1d29ff
    4428 
    4429 > color (#!8 & sel) #5a1d28ff
    4430 
    4431 > color (#!8 & sel) #591c27ff
    4432 
    4433 > color (#!8 & sel) #561c26ff
    4434 
    4435 [Repeated 1 time(s)]
    4436 
    4437 > color (#!8 & sel) #521a24ff
    4438 
    4439 > color (#!8 & sel) #511a24ff
    4440 
    4441 > select clear
    4442 
    4443 > select #8/C
    4444 
    4445 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    4446 
    4447 > color sel #521a24ff
    4448 
    4449 > color sel #8f2e3fff
    4450 
    4451 > color sel #af384eff
    4452 
    4453 > color sel #bb3c53ff
    4454 
    4455 > color sel #c84059ff
    4456 
    4457 > color sel #d6455fff
    4458 
    4459 > color sel #e14864ff
    4460 
    4461 > color sel #e84b67ff
    4462 
    4463 > color sel #ef4d6aff
    4464 
    4465 > color sel #f54f6cff
    4466 
    4467 > color sel #fc5170ff
    4468 
    4469 > color sel #ff5271ff
    4470 
    4471 [Repeated 1 time(s)]
    4472 
    4473 > color sel #f9506eff
    4474 
    4475 > color sel #f24e6bff
    4476 
    4477 > color sel #ef4d6aff
    4478 
    4479 [Repeated 1 time(s)]
    4480 
    4481 > color sel #ee4d6aff
    4482 
    4483 > color sel #e94b67ff
    4484 
    4485 > color sel #e54965ff
    4486 
    4487 > color sel #e54a66ff
    4488 
    4489 > color sel #ec4c69ff
    4490 
    4491 > color sel #ff5271ff
    4492 
    4493 [Repeated 1 time(s)]
    4494 
    4495 > color sel #ff5c6fff
    4496 
    4497 > color sel #ff6577ff
    4498 
    4499 > color sel #ff6a79ff
    4500 
    4501 > color sel #ff6c7cff
    4502 
    4503 > color sel #ff6e7eff
    4504 
    4505 > color sel #ff6f7fff
    4506 
    4507 > color sel #ff707fff
    4508 
    4509 > color sel #ff7180ff
    4510 
    4511 > color sel #ff7281ff
    4512 
    4513 > color sel #ff7282ff
    4514 
    4515 > color sel #ff7382ff
    4516 
    4517 > color sel #ff7482ff
    4518 
    4519 > color sel #ff7483ff
    4520 
    4521 > color sel #ff7582ff
    4522 
    4523 > color sel #ff7683ff
    4524 
    4525 > color sel #ff7883ff
    4526 
    4527 [Repeated 1 time(s)]
    4528 
    4529 > color sel #ff7a84ff
    4530 
    4531 > color sel #ff7b84ff
    4532 
    4533 [Repeated 1 time(s)]
    4534 
    4535 > color sel #ff7c84ff
    4536 
    4537 > color sel #ff7d85ff
    4538 
    4539 > color sel #ff7d84ff
    4540 
    4541 > color sel #ff7d85ff
    4542 
    4543 > color sel #ff7e85ff
    4544 
    4545 > color sel #ff7f85ff
    4546 
    4547 > color sel #ff8086ff
    4548 
    4549 > color sel #ff8087ff
    4550 
    4551 > color sel #ff8187ff
    4552 
    4553 > color sel #ff8288ff
    4554 
    4555 > color sel #ff8489ff
    4556 
    4557 > color sel #ff868bff
    4558 
    4559 > color sel #ff898cff
    4560 
    4561 > color sel #ff8b8dff
    4562 
    4563 > color sel #ff8b8eff
    4564 
    4565 > color sel #ff8b8dff
    4566 
    4567 > color sel #ff8a8dff
    4568 
    4569 > color sel #ff898dff
    4570 
    4571 > color sel #ff888eff
    4572 
    4573 > color sel #ff878dff
    4574 
    4575 > color sel #ff838cff
    4576 
    4577 > color sel #ff828bff
    4578 
    4579 > color sel #ff808aff
    4580 
    4581 > color sel #ff7f8aff
    4582 
    4583 [Repeated 1 time(s)]
    4584 
    4585 > color sel #ff7e8aff
    4586 
    4587 > color sel #ff7d89ff
    4588 
    4589 > color sel #ff7c88ff
    4590 
    4591 > color sel #ff7a88ff
    4592 
    4593 > color sel #ff7a87ff
    4594 
    4595 > color sel #ff7986ff
    4596 
    4597 > color sel #ff7886ff
    4598 
    4599 [Repeated 1 time(s)]
    4600 
    4601 > color sel #ff7785ff
    4602 
    4603 > color sel #ff7484ff
    4604 
    4605 [Repeated 1 time(s)]
    4606 
    4607 > color sel #ff7282ff
    4608 
    4609 > color sel #ff7283ff
    4610 
    4611 > color sel #ff7282ff
    4612 
    4613 [Repeated 1 time(s)]
    4614 
    4615 > color sel #ff7381ff
    4616 
    4617 > color sel #ff737fff
    4618 
    4619 > color sel #ff737dff
    4620 
    4621 > color sel #ff737bff
    4622 
    4623 [Repeated 1 time(s)]
    4624 
    4625 > color sel #ff737aff
    4626 
    4627 [Repeated 1 time(s)]
    4628 
    4629 > color sel #ff7379ff
    4630 
    4631 > color sel #ff7378ff
    4632 
    4633 [Repeated 1 time(s)]
    4634 
    4635 > color sel #ff7377ff
    4636 
    4637 > color sel #ff7376ff
    4638 
    4639 [Repeated 1 time(s)]
    4640 
    4641 > color sel #ff7375ff
    4642 
    4643 > color sel #ff7374ff
    4644 
    4645 > color sel #ff7373ff
    4646 
    4647 > color sel #ff7473ff
    4648 
    4649 > color sel #ff7573ff
    4650 
    4651 > color sel #ff7672ff
    4652 
    4653 > color sel #ff7772ff
    4654 
    4655 [Repeated 1 time(s)]
    4656 
    4657 > color sel #ff7872ff
    4658 
    4659 > color sel #ff7772ff
    4660 
    4661 > color sel #ff7672ff
    4662 
    4663 > color sel #ff7372ff
    4664 
    4665 > color sel #ff7273ff
    4666 
    4667 > color sel #ff7275ff
    4668 
    4669 > color sel #ff7276ff
    4670 
    4671 > color sel #ff7277ff
    4672 
    4673 > color sel #ff7278ff
    4674 
    4675 [Repeated 1 time(s)]
    4676 
    4677 > color sel #ff7279ff
    4678 
    4679 > color sel #ff727aff
    4680 
    4681 [Repeated 1 time(s)]
    4682 
    4683 > color sel #ff727bff
    4684 
    4685 > color sel #ff727cff
    4686 
    4687 > color sel #ff727dff
    4688 
    4689 > color sel #ff737eff
    4690 
    4691 > color sel #ff737fff
    4692 
    4693 [Repeated 1 time(s)]
    4694 
    4695 > color sel #ff7380ff
    4696 
    4697 [Repeated 1 time(s)]
    4698 
    4699 > color sel #ff7381ff
    4700 
    4701 > color sel #ff7382ff
    4702 
    4703 [Repeated 1 time(s)]
    4704 
    4705 > color sel #ff7383ff
    4706 
    4707 > color sel #ff7485ff
    4708 
    4709 > color sel #ff7386ff
    4710 
    4711 > color sel #ff7488ff
    4712 
    4713 > color sel #ff7489ff
    4714 
    4715 > color sel #ff748aff
    4716 
    4717 > color sel #ff748bff
    4718 
    4719 [Repeated 1 time(s)]
    4720 
    4721 > color sel #ff748cff
    4722 
    4723 [Repeated 1 time(s)]
    4724 
    4725 > color sel #ff738dff
    4726 
    4727 > color sel #ff738eff
    4728 
    4729 > color sel #ff7390ff
    4730 
    4731 > color sel #ff7293ff
    4732 
    4733 > color sel #ff7294ff
    4734 
    4735 > color sel #ff7293ff
    4736 
    4737 > color sel #ff7292ff
    4738 
    4739 [Repeated 1 time(s)]
    4740 
    4741 > color sel #ff7392ff
    4742 
    4743 > select clear
    4744 
    4745 > select #8/B
    4746 
    4747 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    4748 
    4749 > color (#!8 & sel) #fe7392ff
    4750 
    4751 > color (#!8 & sel) #e96986ff
    4752 
    4753 > color (#!8 & sel) #b75369ff
    4754 
    4755 > color (#!8 & sel) #9c4659ff
    4756 
    4757 > color (#!8 & sel) #934254ff
    4758 
    4759 > color (#!8 & sel) #924254ff
    4760 
    4761 > color (#!8 & sel) #914153ff
    4762 
    4763 > color (#!8 & sel) #8c3f50ff
    4764 
    4765 > color (#!8 & sel) #843c4cff
    4766 
    4767 > color (#!8 & sel) #823b4aff
    4768 
    4769 > color (#!8 & sel) #813a4aff
    4770 
    4771 [Repeated 1 time(s)]
    4772 
    4773 > color (#!8 & sel) #954355ff
    4774 
    4775 > color (#!8 & sel) #b8536aff
    4776 
    4777 > color (#!8 & sel) #ba546aff
    4778 
    4779 > color (#!8 & sel) #bb546bff
    4780 
    4781 > color (#!8 & sel) #c1576eff
    4782 
    4783 > color (#!8 & sel) #c55971ff
    4784 
    4785 [Repeated 2 time(s)]
    4786 
    4787 > color (#!8 & sel) #c85a72ff
    4788 
    4789 > color (#!8 & sel) #c85a73ff
    4790 
    4791 > color (#!8 & sel) #ca5b74ff
    4792 
    4793 > color (#!8 & sel) #cd5c75ff
    4794 
    4795 > color (#!8 & sel) #cd5d76ff
    4796 
    4797 > color (#!8 & sel) #cc5c75ff
    4798 
    4799 > color (#!8 & sel) #ca5b74ff
    4800 
    4801 [Repeated 1 time(s)]
    4802 
    4803 > color (#!8 & sel) #cb5c75ff
    4804 
    4805 > color (#!8 & sel) #cc5c75ff
    4806 
    4807 > color (#!8 & sel) #cd5c75ff
    4808 
    4809 > color (#!8 & sel) #ce5d76ff
    4810 
    4811 > color (#!8 & sel) #cf5d77ff
    4812 
    4813 > color (#!8 & sel) #d05e77ff
    4814 
    4815 > color (#!8 & sel) #c1153cff
    4816 
    4817 > color (#!8 & sel) #bb3b50ff
    4818 
    4819 > select clear
    4820 
    4821 > select #8/A-C
    4822 
    4823 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    4824 
    4825 > color (#!8 & sel) #bb3c53ff
    4826 
    4827 [Repeated 1 time(s)]
    4828 
    4829 > color (#!8 & sel) #b43a50ff
    4830 
    4831 > color (#!8 & sel) #9c3245ff
    4832 
    4833 > color (#!8 & sel) #8e2e3fff
    4834 
    4835 > color (#!8 & sel) #8b2d3eff
    4836 
    4837 > color (#!8 & sel) #882c3cff
    4838 
    4839 > color (#!8 & sel) #832a3aff
    4840 
    4841 > color (#!8 & sel) #7b2837ff
    4842 
    4843 > color (#!8 & sel) #762634ff
    4844 
    4845 [Repeated 1 time(s)]
    4846 
    4847 > color (#!8 & sel) #67212eff
    4848 
    4849 > color (#!8 & sel) #611f2bff
    4850 
    4851 > color (#!8 & sel) #601f2aff
    4852 
    4853 > color (#!8 & sel) #5c1e29ff
    4854 
    4855 > color (#!8 & sel) #561c26ff
    4856 
    4857 > color (#!8 & sel) #521a25ff
    4858 
    4859 > color (#!8 & sel) #521a24ff
    4860 
    4861 > color (#!8 & sel) #4f1923ff
    4862 
    4863 > color (#!8 & sel) #4d1922ff
    4864 
    4865 > color (#!8 & sel) #4c1922ff
    4866 
    4867 > color (#!8 & sel) #4b1821ff
    4868 
    4869 > color (#!8 & sel) #4a1821ff
    4870 
    4871 > color (#!8 & sel) #481720ff
    4872 
    4873 > color (#!8 & sel) #40151dff
    4874 
    4875 > color (#!8 & sel) #3d141bff
    4876 
    4877 > color (#!8 & sel) #3b131aff
    4878 
    4879 > color (#!8 & sel) #351117ff
    4880 
    4881 > color (#!8 & sel) #2d0e14ff
    4882 
    4883 > color (#!8 & sel) #2c0e14ff
    4884 
    4885 > color (#!8 & sel) #280d12ff
    4886 
    4887 > color (#!8 & sel) #220b0fff
    4888 
    4889 > color (#!8 & sel) #1b090cff
    4890 
    4891 > color (#!8 & sel) #1c090cff
    4892 
    4893 > color (#!8 & sel) #300f15ff
    4894 
    4895 > color (#!8 & sel) #5e1e2aff
    4896 
    4897 > color (#!8 & sel) #712432ff
    4898 
    4899 > color (#!8 & sel) #7a2736ff
    4900 
    4901 > color (#!8 & sel) #802939ff
    4902 
    4903 > color (#!8 & sel) #8c2d3eff
    4904 
    4905 > color (#!8 & sel) #943042ff
    4906 
    4907 > color (#!8 & sel) #9c3245ff
    4908 
    4909 > color (#!8 & sel) #a13447ff
    4910 
    4911 > color (#!8 & sel) #a63549ff
    4912 
    4913 > color (#!8 & sel) #ab374cff
    4914 
    4915 > color (#!8 & sel) #af384eff
    4916 
    4917 [Repeated 1 time(s)]
    4918 
    4919 > color (#!8 & sel) #9a3244ff
    4920 
    4921 > color (#!8 & sel) #902e40ff
    4922 
    4923 > color (#!8 & sel) #8d2d3fff
    4924 
    4925 > color (#!8 & sel) #8c2d3eff
    4926 
    4927 > color (#!8 & sel) #832a3aff
    4928 
    4929 > color (#!8 & sel) #7f2938ff
    4930 
    4931 > select clear
    4932 
    4933 > select #8/B
    4934 
    4935 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    4936 
    4937 > color (#!8 & sel) #7f2938ff
    4938 
    4939 > color (#!8 & sel) #8e2e3fff
    4940 
    4941 > color (#!8 & sel) #9b3245ff
    4942 
    4943 > color (#!8 & sel) #a33448ff
    4944 
    4945 > color (#!8 & sel) #b1394eff
    4946 
    4947 > color (#!8 & sel) #b73b51ff
    4948 
    4949 > color (#!8 & sel) #b93b52ff
    4950 
    4951 > color (#!8 & sel) #ba3c52ff
    4952 
    4953 > color (#!8 & sel) #d84560ff
    4954 
    4955 > color (#!8 & sel) #ff5271ff
    4956 
    4957 > select clear
    4958 
    4959 > select #8/C
    4960 
    4961 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    4962 
    4963 > color sel #ff566bff
    4964 
    4965 > color sel #ff576bff
    4966 
    4967 > color sel #ff576cff
    4968 
    4969 > color sel #ff586dff
    4970 
    4971 > color sel #ff5a6fff
    4972 
    4973 > color sel #ff5c71ff
    4974 
    4975 > color sel #ff5e73ff
    4976 
    4977 > color sel #ff5f75ff
    4978 
    4979 > color sel #ff6277ff
    4980 
    4981 > color sel #ff6278ff
    4982 
    4983 > color sel #ff6479ff
    4984 
    4985 > color sel #ff647aff
    4986 
    4987 > color sel #ff657bff
    4988 
    4989 > color sel #ff667bff
    4990 
    4991 > color sel #ff667cff
    4992 
    4993 > color sel #ff677dff
    4994 
    4995 > color sel #ff687dff
    4996 
    4997 > color sel #ff697eff
    4998 
    4999 > color sel #ff6a80ff
    5000 
    5001 > color sel #ff6b80ff
    5002 
    5003 > color sel #ff6c82ff
    5004 
    5005 > color sel #ff6d82ff
    5006 
    5007 > color sel #ff7388ff
    5008 
    5009 > color sel #ff7389ff
    5010 
    5011 > color sel #ff758bff
    5012 
    5013 > color sel #ff778dff
    5014 
    5015 > color sel #ff788eff
    5016 
    5017 > color sel #ff7a90ff
    5018 
    5019 > color sel #ff7c92ff
    5020 
    5021 > color sel #ff7e95ff
    5022 
    5023 > color sel #ff7f95ff
    5024 
    5025 > color sel #ff8198ff
    5026 
    5027 > color sel #ff8298ff
    5028 
    5029 > color sel #ff8299ff
    5030 
    5031 > color sel #ff849bff
    5032 
    5033 > color sel #ff879eff
    5034 
    5035 > color sel #ff879fff
    5036 
    5037 > color sel #ff89a0ff
    5038 
    5039 > color sel #ff8aa2ff
    5040 
    5041 > color sel #ff8ba2ff
    5042 
    5043 > color sel #ff8ba3ff
    5044 
    5045 > color sel #ff8ca4ff
    5046 
    5047 > color sel #ff8da4ff
    5048 
    5049 > color sel #ff8fa7ff
    5050 
    5051 > color sel #ff90a8ff
    5052 
    5053 > color sel #ff91a9ff
    5054 
    5055 > color sel #ff91aaff
    5056 
    5057 > select clear
    5058 
    5059 > select #8/C
    5060 
    5061 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    5062 
    5063 > color sel #ff8fa7ff
    5064 
    5065 > select clear
    5066 
    5067 > undo
    5068 
    5069 > select clear
    5070 
    5071 > select #8/A-C
    5072 
    5073 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    5074 
    5075 > select #8/A
    5076 
    5077 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    5078 
    5079 > color (#!8 & sel) #c1153cff
    5080 
    5081 > color (#!8 & sel) #be3c51ff
    5082 
    5083 > color (#!8 & sel) #ba3a4fff
    5084 
    5085 > color (#!8 & sel) #a83548ff
    5086 
    5087 > color (#!8 & sel) #9c3142ff
    5088 
    5089 > color (#!8 & sel) #952f40ff
    5090 
    5091 > color (#!8 & sel) #8d2c3cff
    5092 
    5093 > color (#!8 & sel) #862a39ff
    5094 
    5095 > color (#!8 & sel) #852a39ff
    5096 
    5097 > color (#!8 & sel) #842938ff
    5098 
    5099 > color (#!8 & sel) #832938ff
    5100 
    5101 [Repeated 1 time(s)]
    5102 
    5103 > color (#!8 & sel) #812837ff
    5104 
    5105 > color (#!8 & sel) #802837ff
    5106 
    5107 > color (#!8 & sel) #802836ff
    5108 
    5109 > color (#!8 & sel) #792634ff
    5110 
    5111 > color (#!8 & sel) #782533ff
    5112 
    5113 > color (#!8 & sel) #762532ff
    5114 
    5115 > color (#!8 & sel) #742431ff
    5116 
    5117 > color (#!8 & sel) #702330ff
    5118 
    5119 > color (#!8 & sel) #6e232fff
    5120 
    5121 > color (#!8 & sel) #6d222fff
    5122 
    5123 > color (#!8 & sel) #6c222eff
    5124 
    5125 [Repeated 1 time(s)]
    5126 
    5127 > color (#!8 & sel) #6d222eff
    5128 
    5129 > color (#!8 & sel) #6e232fff
    5130 
    5131 > color (#!8 & sel) #6f232fff
    5132 
    5133 > color (#!8 & sel) #702330ff
    5134 
    5135 [Repeated 1 time(s)]
    5136 
    5137 > select clear
    5138 
    5139 > select #8/A
    5140 
    5141 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    5142 
    5143 > color (#!8 & sel) #c1153cff
    5144 
    5145 > color (#!8 & sel) #be3c51ff
    5146 
    5147 > color (#!8 & sel) #be3b51ff
    5148 
    5149 > color (#!8 & sel) #b3384cff
    5150 
    5151 > color (#!8 & sel) #a63447ff
    5152 
    5153 > color (#!8 & sel) #9d3143ff
    5154 
    5155 > color (#!8 & sel) #942e3fff
    5156 
    5157 > color (#!8 & sel) #902d3dff
    5158 
    5159 > color (#!8 & sel) #8a2b3bff
    5160 
    5161 > color (#!8 & sel) #802836ff
    5162 
    5163 > color (#!8 & sel) #772533ff
    5164 
    5165 > color (#!8 & sel) #702330ff
    5166 
    5167 > color (#!8 & sel) #6b222eff
    5168 
    5169 > color (#!8 & sel) #67202cff
    5170 
    5171 > color (#!8 & sel) #641f2bff
    5172 
    5173 > color (#!8 & sel) #631f2aff
    5174 
    5175 [Repeated 1 time(s)]
    5176 
    5177 > color (#!8 & sel) #611e29ff
    5178 
    5179 > color (#!8 & sel) #5d1d27ff
    5180 
    5181 > color (#!8 & sel) #581c25ff
    5182 
    5183 > color (#!8 & sel) #571b25ff
    5184 
    5185 [Repeated 1 time(s)]
    5186 
    5187 > color (#!8 & sel) #591c26ff
    5188 
    5189 > color (#!8 & sel) #5c1d27ff
    5190 
    5191 > color (#!8 & sel) #611e29ff
    5192 
    5193 > color (#!8 & sel) #67202cff
    5194 
    5195 > color (#!8 & sel) #712330ff
    5196 
    5197 > color (#!8 & sel) #742432ff
    5198 
    5199 > color (#!8 & sel) #752532ff
    5200 
    5201 > color (#!8 & sel) #722431ff
    5202 
    5203 > color (#!8 & sel) #712430ff
    5204 
    5205 > color (#!8 & sel) #702330ff
    5206 
    5207 [Repeated 1 time(s)]
    5208 
    5209 > color (#!8 & sel) #6d222fff
    5210 
    5211 > color (#!8 & sel) #6c222eff
    5212 
    5213 [Repeated 1 time(s)]
    5214 
    5215 > color (#!8 & sel) #6b222eff
    5216 
    5217 [Repeated 1 time(s)]
    5218 
    5219 > color (#!8 & sel) #6b212dff
    5220 
    5221 > color (#!8 & sel) #6a212dff
    5222 
    5223 [Repeated 2 time(s)]
    5224 
    5225 > color (#!8 & sel) #69212dff
    5226 
    5227 [Repeated 1 time(s)]
    5228 
    5229 > select clear
    5230 
    5231 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    5232 
    5233 > select #8/A-C
    5234 
    5235 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    5236 Alignment identifier is 1 
    5237 
    5238 > select #8/C:469
    5239 
    5240 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5241 
    5242 > select #8/C:469-473
    5243 
    5244 48 atoms, 47 bonds, 5 residues, 1 model selected 
    5245 
    5246 > select #8/C:475
    5247 
    5248 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5249 
    5250 > select #8/C:475-485
    5251 
    5252 92 atoms, 92 bonds, 11 residues, 1 model selected 
    5253 
    5254 > select #8/A-C:491
    5255 
    5256 21 atoms, 18 bonds, 3 residues, 1 model selected 
    5257 
    5258 > select #8/A-C:491-572
    5259 
    5260 2013 atoms, 2049 bonds, 246 residues, 1 model selected 
    5261 
    5262 > select clear
    5263 
    5264 > view name front
    5265 
    5266 > rotate 90 y
    5267 
    5268 Unknown command: rotate 90 y 
    5269 
    5270 > rotate y 90
    5271 
    5272 Unknown command: rotate y 90 
    5273 
    5274 > rotate
    5275 
    5276 Unknown command: rotate 
    5277 
    5278 > turn y 90
    5279 
    5280 > turn z 90
    5281 
    5282 > turn x 90
    5283 
    5284 > view front
    5285 
    5286 > ui tool show "Side View"
    5287 
    5288 > view name front
    5289 
    5290 > turn x 90
    5291 
    5292 > view front
    5293 
    5294 > turn x 90
    5295 
    5296 > view name front
    5297 
    5298 [Repeated 1 time(s)]
    5299 
    5300 > turn x 90
    5301 
    5302 > hide #!8 models
    5303 
    5304 > transparency #2,3,7 0
    5305 
    5306 > transparency #2,3,7 70
    5307 
    5308 > movie record size info
    5309 
    5310 Invalid "size" argument: Expected an integer 
    5311 
    5312 > lighting soft
    5313 
    5314 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    5315 
    5316 ——— End of log from Mon Jun 9 23:00:16 2025 ———
    5317 
    5318 opened ChimeraX session 
    5319 
    5320 > view front
    5321 
    5322 > transparency #2,3,7 40
    5323 
    5324 > transparency #2,3,7 60
    5325 
    5326 > transparency #2,3,7 80
    5327 
    5328 > transparency #2,3,7 30
    5329 
    5330 > transparency #2,3,7 10
    5331 
    5332 > view front
    5333 
    5334 > graphics silhouettes true
    5335 
    5336 > lighting depthCue false
    5337 
    5338 > lighting soft
    5339 
    5340 > graphics bgColor white
    5341 
    5342 > show #!8 models
    5343 
    5344 > hide #!8 models
    5345 
    5346 > show #!8 models
    5347 
    5348 > hide #!8 models
    5349 
    5350 > transparency #2 10
    5351 
    5352 > transparency #2 0
    5353 
    5354 > transparency #3 0
    5355 
    5356 > transparency #7 0
    5357 
    5358 > transparency #7 60
    5359 
    5360 > hide #!8 models
    5361 
    5362 > transparency #7 0
    5363 
    5364 > transparency #3 30
    5365 
    5366 > transparency #3 50
    5367 
    5368 > transparency #3 10
    5369 
    5370 > show #!8 models
    5371 
    5372 > hide #!8 models
    5373 
    5374 > transparency #3,2,7 10
    5375 
    5376 > lightling gent;le
    5377 
    5378 Unknown command: lightling gent;le 
    5379 
    5380 > lightling gente
    5381 
    5382 Unknown command: lightling gente 
    5383 
    5384 > lightling gentle
    5385 
    5386 Unknown command: lightling gentle 
    5387 
    5388 > lighting gentle
    5389 
    5390 > transparency #3,2,7 60
    5391 
    5392 > show #!8 models
    5393 
    5394 > transparency #3,2,7 50
    5395 
    5396 > transparency #3,2,7 65
    5397 
    5398 > lighting soft
    5399 
    5400 > transparency #3,2,7 68
    5401 
    5402 > lighting gentle
    5403 
    5404 > view frony
    5405 
    5406 Expected an objects specifier or a view name or a keyword 
    5407 
    5408 > view front
    5409 
    5410 > hide #!8 models
    5411 
    5412 > transparency #3,2,7 0
    5413 
    5414 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    5415 > supersample 4 transparentBackground true
    5416 
    5417 [Repeated 1 time(s)]
    5418 
    5419 > transparency #3,2,7 68
    5420 
    5421 > show #!8 models
    5422 
    5423 > view name front
    5424 
    5425 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    5426 > supersample 4
    5427 
    5428 > color #7 #8c8dfcff models
    5429 
    5430 > color #3 #8c8dfcff models
    5431 
    5432 > color #2 #8c8dfcff models
    5433 
    5434 > transparency #3,2,7 68
    5435 
    5436 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    5437 > supersample 4
    5438 
    5439 > hide #!8 models
    5440 
    5441 > transparency #3,2,7 0
    5442 
    5443 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    5444 > supersample 4 transparentBackground true
    5445 
    5446 > color #3 #a3a7ffff models
    5447 
    5448 > color #2 #a3a7ffff models
    5449 
    5450 > color #7 #a3a7ffff models
    5451 
    5452 > color #7 #b5bcffff models
    5453 
    5454 > color #3 #b5bcffff models
    5455 
    5456 > color #2 #b5bcffff models
    5457 
    5458 > color #2 #7a81ffff models
    5459 
    5460 > color #3 #7a81ffff models
    5461 
    5462 > transparency #3,2,7 68
    5463 
    5464 > transparency #3,2,7 0
    5465 
    5466 > transparency #3,2,7 68
    5467 
    5468 > show #!8 models
    5469 
    5470 > color #7 #c4caffff models
    5471 
    5472 > transparency #3,2,7 0
    5473 
    5474 > color #3 #919affff models
    5475 
    5476 > color #7 #7a81ffff models
    5477 
    5478 > color #7 #919affff models
    5479 
    5480 > color #2 #919affff models
    5481 
    5482 > color #7 #a8b2ffff models
    5483 
    5484 > color #3 #a8b2ffff models
    5485 
    5486 > color #2 #a8b2ffff models
    5487 
    5488 > transparency #3,2,7 68
    5489 
    5490 > transparency #3,2,7 0
    5491 
    5492 > transparency #3,2,7 68
    5493 
    5494 > transparency #3,2,7 0
    5495 
    5496 > hide #!8 models
    5497 
    5498 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    5499 > supersample 4 transparentBackground true
    5500 
    5501 > transparency #3,2,7 68
    5502 
    5503 > show #!8 models
    5504 
    5505 > transparency #3,2,7 69
    5506 
    5507 > transparency #3,2,7 70
    5508 
    5509 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    5510 > supersample 4
    5511 
    5512 > transparency #3,2,7 20
    5513 
    5514 > transparency #3,2,7 30
    5515 
    5516 > usage vop
    5517 
    5518 vop [optional] 
    5519 — alias of "volume $*" 
    5520 optional: the rest of line 
    5521 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    5522 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    5523 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    5524 a number] [transparency a number] [appearance appearance] [nameAppearance a
    5525 text string] [nameForget nameForget] [step map step] [region map region]
    5526 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    5527 floats] [voxelSize 1 or 3 floats] [planes planes
    5528 x|y|z[,[,[,[,]]]]] [dumpHeader true or false]
    5529 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    5530 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    5531 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    5532 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    5533 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    5534 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    5535 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    5536 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    5537 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    5538 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    5539 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    5540 [fullRegionOnGpu true or false] [btCorrection true or false]
    5541 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    5542 false] [linearInterpolation true or false] [dimTransparency true or false]
    5543 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    5544 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    5545 [subdivideSurface true or false] [subdivisionLevels an integer]
    5546 [surfaceSmoothing true or false] [smoothingIterations an integer]
    5547 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    5548 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    5549 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    5550 an integer] [backingColor backingColor] 
    5551 — set volume model parameters, display style and colors 
    5552 style: one of image, mesh, solid, or surface 
    5553 change: one of image or surface 
    5554 close: one of image or surface 
    5555 level: some numbers, repeatable 
    5556 rmsLevel: some numbers, repeatable 
    5557 sdLevel: some numbers, repeatable 
    5558 encloseVolume: some numbers 
    5559 fastEncloseVolume: some numbers 
    5560 color: a color, repeatable 
    5561 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5562 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5563 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5564 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5565 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5566 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5567 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5568 Bone 
    5569 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5570 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5571 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5572 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5573 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5574 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5575 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5576 Bone 
    5577 orthoplanes: one of off, xy, xyz, xz, or yz 
    5578 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    5579 initialColors: some colors 
    5580 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    5581 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    5582 rgba12, rgba16, rgba4, or rgba8 
    5583 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    5584 planeSpacing: one of max, mean, or min or a number 
    5585 positionPlanes: 3-tuple of integers 
    5586 backingColor: a color or none 
    5587 Subcommands are:
    5588 
    5589   * volume add
    5590   * volume bin
    5591   * volume boxes
    5592   * volume channels
    5593   * volume copy
    5594   * volume cover
    5595   * volume defaultvalues
    5596   * volume erase
    5597   * volume falloff
    5598   * volume flatten
    5599   * volume flip
    5600   * volume fourier
    5601   * volume gaussian
    5602   * volume laplacian
    5603   * volume localCorrelation
    5604   * volume mask
    5605   * volume maximum
    5606   * volume median
    5607   * volume minimum
    5608   * volume morph
    5609   * volume multiply
    5610   * volume new
    5611   * volume octant
    5612   * volume ~octant
    5613   * volume onesmask
    5614   * volume permuteAxes
    5615   * volume resample
    5616   * volume ridges
    5617   * volume scale
    5618   * volume settings
    5619   * volume sharpen
    5620   * volume splitbyzone
    5621   * volume subtract
    5622   * volume threshold
    5623   * volume tile
    5624   * volume unbend
    5625   * volume unroll
    5626   * volume unzone
    5627   * volume zone
    5628 
    5629  
    5630 
    5631 > hide #!7 models
    5632 
    5633 > show #!7 models
    5634 
    5635 > hide #!3 models
    5636 
    5637 > show #!3 models
    5638 
    5639 > vop copy #3
    5640 
    5641 Opened emd_51808.map copy as #9, grid size 500,500,500, pixel 1.35, shown at
    5642 step 1, values float32 
    5643 
    5644 > show #!3 models
    5645 
    5646 > hide #!3 models
    5647 
    5648 > show #!3 models
    5649 
    5650 > hide #!3 models
    5651 
    5652 > show #!3 models
    5653 
    5654 > hide #!3 models
    5655 
    5656 > usage vop
    5657 
    5658 vop [optional] 
    5659 — alias of "volume $*" 
    5660 optional: the rest of line 
    5661 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    5662 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    5663 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    5664 a number] [transparency a number] [appearance appearance] [nameAppearance a
    5665 text string] [nameForget nameForget] [step map step] [region map region]
    5666 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    5667 floats] [voxelSize 1 or 3 floats] [planes planes
    5668 x|y|z[,[,[,[,]]]]] [dumpHeader true or false]
    5669 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    5670 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    5671 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    5672 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    5673 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    5674 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    5675 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    5676 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    5677 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    5678 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    5679 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    5680 [fullRegionOnGpu true or false] [btCorrection true or false]
    5681 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    5682 false] [linearInterpolation true or false] [dimTransparency true or false]
    5683 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    5684 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    5685 [subdivideSurface true or false] [subdivisionLevels an integer]
    5686 [surfaceSmoothing true or false] [smoothingIterations an integer]
    5687 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    5688 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    5689 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    5690 an integer] [backingColor backingColor] 
    5691 — set volume model parameters, display style and colors 
    5692 style: one of image, mesh, solid, or surface 
    5693 change: one of image or surface 
    5694 close: one of image or surface 
    5695 level: some numbers, repeatable 
    5696 rmsLevel: some numbers, repeatable 
    5697 sdLevel: some numbers, repeatable 
    5698 encloseVolume: some numbers 
    5699 fastEncloseVolume: some numbers 
    5700 color: a color, repeatable 
    5701 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5702 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5703 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5704 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5705 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5706 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5707 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5708 Bone 
    5709 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5710 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5711 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5712 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5713 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5714 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5715 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5716 Bone 
    5717 orthoplanes: one of off, xy, xyz, xz, or yz 
    5718 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    5719 initialColors: some colors 
    5720 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    5721 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    5722 rgba12, rgba16, rgba4, or rgba8 
    5723 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    5724 planeSpacing: one of max, mean, or min or a number 
    5725 positionPlanes: 3-tuple of integers 
    5726 backingColor: a color or none 
    5727 Subcommands are:
    5728 
    5729   * volume add
    5730   * volume bin
    5731   * volume boxes
    5732   * volume channels
    5733   * volume copy
    5734   * volume cover
    5735   * volume defaultvalues
    5736   * volume erase
    5737   * volume falloff
    5738   * volume flatten
    5739   * volume flip
    5740   * volume fourier
    5741   * volume gaussian
    5742   * volume laplacian
    5743   * volume localCorrelation
    5744   * volume mask
    5745   * volume maximum
    5746   * volume median
    5747   * volume minimum
    5748   * volume morph
    5749   * volume multiply
    5750   * volume new
    5751   * volume octant
    5752   * volume ~octant
    5753   * volume onesmask
    5754   * volume permuteAxes
    5755   * volume resample
    5756   * volume ridges
    5757   * volume scale
    5758   * volume settings
    5759   * volume sharpen
    5760   * volume splitbyzone
    5761   * volume subtract
    5762   * volume threshold
    5763   * volume tile
    5764   * volume unbend
    5765   * volume unroll
    5766   * volume unzone
    5767   * volume zone
    5768 
    5769  
    5770 
    5771 > volume zone #9 nearAtoms #8
    5772 
    5773 > hide #!7 models
    5774 
    5775 > hide #!2 models
    5776 
    5777 > show #!3 models
    5778 
    5779 > show #!2 models
    5780 
    5781 > usage vop
    5782 
    5783 vop [optional] 
    5784 — alias of "volume $*" 
    5785 optional: the rest of line 
    5786 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    5787 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    5788 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    5789 a number] [transparency a number] [appearance appearance] [nameAppearance a
    5790 text string] [nameForget nameForget] [step map step] [region map region]
    5791 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    5792 floats] [voxelSize 1 or 3 floats] [planes planes
    5793 x|y|z[,[,[,[,]]]]] [dumpHeader true or false]
    5794 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    5795 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    5796 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    5797 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    5798 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    5799 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    5800 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    5801 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    5802 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    5803 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    5804 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    5805 [fullRegionOnGpu true or false] [btCorrection true or false]
    5806 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    5807 false] [linearInterpolation true or false] [dimTransparency true or false]
    5808 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    5809 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    5810 [subdivideSurface true or false] [subdivisionLevels an integer]
    5811 [surfaceSmoothing true or false] [smoothingIterations an integer]
    5812 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    5813 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    5814 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    5815 an integer] [backingColor backingColor] 
    5816 — set volume model parameters, display style and colors 
    5817 style: one of image, mesh, solid, or surface 
    5818 change: one of image or surface 
    5819 close: one of image or surface 
    5820 level: some numbers, repeatable 
    5821 rmsLevel: some numbers, repeatable 
    5822 sdLevel: some numbers, repeatable 
    5823 encloseVolume: some numbers 
    5824 fastEncloseVolume: some numbers 
    5825 color: a color, repeatable 
    5826 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5827 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5828 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5829 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5830 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5831 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5832 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5833 Bone 
    5834 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    5835 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    5836 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    5837 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    5838 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    5839 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    5840 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    5841 Bone 
    5842 orthoplanes: one of off, xy, xyz, xz, or yz 
    5843 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    5844 initialColors: some colors 
    5845 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    5846 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    5847 rgba12, rgba16, rgba4, or rgba8 
    5848 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    5849 planeSpacing: one of max, mean, or min or a number 
    5850 positionPlanes: 3-tuple of integers 
    5851 backingColor: a color or none 
    5852 Subcommands are:
    5853 
    5854   * volume add
    5855   * volume bin
    5856   * volume boxes
    5857   * volume channels
    5858   * volume copy
    5859   * volume cover
    5860   * volume defaultvalues
    5861   * volume erase
    5862   * volume falloff
    5863   * volume flatten
    5864   * volume flip
    5865   * volume fourier
    5866   * volume gaussian
    5867   * volume laplacian
    5868   * volume localCorrelation
    5869   * volume mask
    5870   * volume maximum
    5871   * volume median
    5872   * volume minimum
    5873   * volume morph
    5874   * volume multiply
    5875   * volume new
    5876   * volume octant
    5877   * volume ~octant
    5878   * volume onesmask
    5879   * volume permuteAxes
    5880   * volume resample
    5881   * volume ridges
    5882   * volume scale
    5883   * volume settings
    5884   * volume sharpen
    5885   * volume splitbyzone
    5886   * volume subtract
    5887   * volume threshold
    5888   * volume tile
    5889   * volume unbend
    5890   * volume unroll
    5891   * volume unzone
    5892   * volume zone
    5893 
    5894  
    5895 
    5896 > vop copy #3
    5897 
    5898 Opened emd_51808.map copy as #10, grid size 500,500,500, pixel 1.35, shown at
    5899 step 1, values float32 
    5900 
    5901 > vop subtract #10 #9
    5902 
    5903 Opened volume difference as #11, grid size 500,500,500, pixel 1.35, shown at
    5904 step 1, values float32 
    5905 
    5906 > show #!10 models
    5907 
    5908 > hide #!10 models
    5909 
    5910 > hide #!2 models
    5911 
    5912 > show #!2 models
    5913 
    5914 > show #!3 models
    5915 
    5916 > hide #!3 models
    5917 
    5918 > show #!7 models
    5919 
    5920 > show #!9 models
    5921 
    5922 > hide #!9 models
    5923 
    5924 > show #!9 models
    5925 
    5926 > show #!10 models
    5927 
    5928 > hide #!9 models
    5929 
    5930 > show #!9 models
    5931 
    5932 > hide #!9 models
    5933 
    5934 > hide #!11 models
    5935 
    5936 > show #!11 models
    5937 
    5938 > hide #!10 models
    5939 
    5940 > select add #11
    5941 
    5942 2 models selected 
    5943 
    5944 > select subtract #11
    5945 
    5946 Nothing selected 
    5947 
    5948 > select add #11
    5949 
    5950 2 models selected 
    5951 
    5952 > select subtract #11
    5953 
    5954 Nothing selected 
    5955 
    5956 > hide #11.1 models
    5957 
    5958 > show #11.1 models
    5959 
    5960 > hide #!11 models
    5961 
    5962 > show #!11 models
    5963 
    5964 > volume #11 level -0.2366
    5965 
    5966 > volume #11 level -0.8872
    5967 
    5968 > close #11
    5969 
    5970 > show #!10 models
    5971 
    5972 > volume zone #9 nearAtoms #8 invert true
    5973 
    5974 volume zone command currently does not support invert True with newMap False 
    5975 
    5976 > volume zone #9 nearAtoms #8 invert true newMap true
    5977 
    5978 Opened emd_51808.map copy zone as #11, grid size 500,500,500, pixel 1.35,
    5979 shown at step 1, values float32 
    5980 
    5981 > hide #!7 models
    5982 
    5983 > hide #!2 models
    5984 
    5985 > show #!2 models
    5986 
    5987 > show #!3 models
    5988 
    5989 > hide #!3 models
    5990 
    5991 > show #!7 models
    5992 
    5993 > hide #!7 models
    5994 
    5995 > show #!7 models
    5996 
    5997 > hide #!7 models
    5998 
    5999 > show #!7 models
    6000 
    6001 > hide #!8 models
    6002 
    6003 > show #!8 models
    6004 
    6005 > hide #!10 models
    6006 
    6007 > show #!10 models
    6008 
    6009 > hide #!11 models
    6010 
    6011 > hide #!7 models
    6012 
    6013 > show #!7 models
    6014 
    6015 > hide #!10 models
    6016 
    6017 > show #!10 models
    6018 
    6019 > close #10
    6020 
    6021 > show #!9 models
    6022 
    6023 > show #!11 models
    6024 
    6025 > transparency #9 70
    6026 
    6027 > transparency #9 50
    6028 
    6029 > hide #8.1 models
    6030 
    6031 > show #8.1 models
    6032 
    6033 > volume zone #9 nearAtoms #8/A-C
    6034 
    6035 > hide #!9 models
    6036 
    6037 > show #!9 models
    6038 
    6039 > hide #!7 models
    6040 
    6041 > show #!7 models
    6042 
    6043 > hide #!9 models
    6044 
    6045 > show #!9 models
    6046 
    6047 > hide #!11 models
    6048 
    6049 > show #!11 models
    6050 
    6051 > close #11
    6052 
    6053 > show #!3 models
    6054 
    6055 > hide #!3 models
    6056 
    6057 > volume zone #9 nearAtoms #8/A-C invert true newMap true
    6058 
    6059 Opened emd_51808.map copy zone as #10, grid size 500,500,500, pixel 1.35,
    6060 shown at step 1, values float32 
    6061 
    6062 > color #10 #a8b2ffff models
    6063 
    6064 > transparency #2,7,10 0
    6065 
    6066 > show #!9 models
    6067 
    6068 > transparency #9 70
    6069 
    6070 > view front
    6071 
    6072 > color #10 #b9c2ffff models
    6073 
    6074 > undo
    6075 
    6076 > color #10 #a8b2ffff models
    6077 
    6078 > hide #!10 models
    6079 
    6080 > show #!10 models
    6081 
    6082 > color #10 #dbd3beff models
    6083 
    6084 > color #10 #d2d2d3ff models
    6085 
    6086 > color #10 #dfd9fcff models
    6087 
    6088 > color #10 #75ff79ff models
    6089 
    6090 > color #10 #c2cafdff models
    6091 
    6092 > color #10 #3b8fffff models
    6093 
    6094 > color #10 #f8ccb1ff models
    6095 
    6096 > color #10 #f8c2a6ff models
    6097 
    6098 > color #10 #257bf8ff models
    6099 
    6100 > color #10 #f8e153ff models
    6101 
    6102 > color #10 #f88690ff models
    6103 
    6104 > color #10 #f8cef5ff models
    6105 
    6106 > color #10 #e8f8c3ff models
    6107 
    6108 > color #10 #e8f8c1ff models
    6109 
    6110 > color #10 #f8eb15ff models
    6111 
    6112 > color #10 #f8c97eff models
    6113 
    6114 > color #10 #b2c5f8ff models
    6115 
    6116 > color #10 #d3c0f8ff models
    6117 
    6118 > color #10 #f7f8f4ff models
    6119 
    6120 > color #10 #f7f8f3ff models
    6121 
    6122 > color #10 #f8ae8eff models
    6123 
    6124 > color #10 #edf8f4ff models
    6125 
    6126 > color #10 #d3f8cdff models
    6127 
    6128 > color #10 #b4f8e9ff models
    6129 
    6130 > color #10 #a8b2ffff models
    6131 
    6132 > color #10 #b9c2ffff models
    6133 
    6134 > color #9 #b9c2ffff models
    6135 
    6136 > color #7 #b9c2ffff models
    6137 
    6138 > color #2 #b9c2ffff models
    6139 
    6140 > transparency #9 70
    6141 
    6142 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    6143 
    6144 > hide #!10 models
    6145 
    6146 > show #!3 models
    6147 
    6148 > measure symmetry #3
    6149 
    6150 Symmetry emd_51808.map: C2, center 250 250 258 
    6151 
    6152 > hide #!9 models
    6153 
    6154 > show #!9 models
    6155 
    6156 > close #9
    6157 
    6158 > close #10
    6159 
    6160 > hide #!8 models
    6161 
    6162 > show #!8 models
    6163 
    6164 > hide #!8 models
    6165 
    6166 > hide #!3 models
    6167 
    6168 > show #!3 models
    6169 
    6170 > hide #!3 models
    6171 
    6172 > show #!3 models
    6173 
    6174 > show #!8 models
    6175 
    6176 > combine #8
    6177 
    6178 > hide #!9 models
    6179 
    6180 > show #!9 models
    6181 
    6182 > select add #9
    6183 
    6184 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6185 
    6186 > ui mousemode right "translate selected models"
    6187 
    6188 > view matrix models
    6189 > #9,-0.98735,-0.15852,-0.003891,712.94,0.15825,-0.98356,-0.087032,715.49,0.009969,-0.086547,0.9962,8.7721
    6190 
    6191 > ui tool show "Fit in Map"
    6192 
    6193 > fitmap #9 inMap #3
    6194 
    6195 Fit molecule copy of 8i8b (#9) to map emd_51808.map (#3) using 30015 atoms 
    6196 average map value = 0.007136, steps = 320 
    6197 shifted from previous position = 31.9 
    6198 rotated from previous position = 25.7 degrees 
    6199 atoms outside contour = 16519, contour level = 0.0074163 
    6200  
    6201 Position of copy of 8i8b (#9) relative to emd_51808.map (#3) coordinates: 
    6202 Matrix rotation and translation 
    6203 -0.94925344 0.31237697 0.03658660 582.26413479 
    6204 -0.31435289 -0.94603362 -0.07875704 874.59558896 
    6205 0.01001027 -0.08626150 0.99622226 15.44026964 
    6206 Axis -0.01196239 0.04236365 -0.99903064 
    6207 Axis point 361.41668086 390.72405261 0.00000000 
    6208 Rotation angle (degrees) 161.71951979 
    6209 Shift along axis 14.66049209 
    6210  
    6211 
    6212 > combine #8
    6213 
    6214 > select add #10
    6215 
    6216 60030 atoms, 61358 bonds, 20 pseudobonds, 7320 residues, 4 models selected 
    6217 
    6218 > select subtract #9
    6219 
    6220 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6221 
    6222 > view matrix models
    6223 > #10,-0.98735,-0.15852,-0.003891,885.33,0.15825,-0.98356,-0.087032,688.64,0.009969,-0.086547,0.9962,7.0211
    6224 
    6225 > fitmap #10 inMap #3
    6226 
    6227 Fit molecule copy of 8i8b (#10) to map emd_51808.map (#3) using 30015 atoms 
    6228 average map value = 0.007154, steps = 280 
    6229 shifted from previous position = 14 
    6230 rotated from previous position = 25.7 degrees 
    6231 atoms outside contour = 16474, contour level = 0.0074163 
    6232  
    6233 Position of copy of 8i8b (#10) relative to emd_51808.map (#3) coordinates: 
    6234 Matrix rotation and translation 
    6235 -0.83743424 -0.54513643 -0.03911764 910.14305591 
    6236 0.54644743 -0.83384401 -0.07809876 480.97407992 
    6237 0.00995647 -0.08677832 0.99617791 15.61062317 
    6238 Axis -0.00794307 -0.04491002 0.99895946 
    6239 Axis point 383.64334273 376.27006042 0.00000000 
    6240 Rotation angle (degrees) 146.88231983 
    6241 Shift along axis -13.23550244 
    6242  
    6243 
    6244 > combine #8
    6245 
    6246 > select subtract #10
    6247 
    6248 Nothing selected 
    6249 
    6250 > select add #11
    6251 
    6252 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6253 
    6254 > view matrix models
    6255 > #11,-0.98735,-0.15852,-0.003891,647.49,0.15825,-0.98356,-0.087032,725.68,0.009969,-0.086547,0.9962,9.1834
    6256 
    6257 > fitmap #11 inMap #3
    6258 
    6259 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6260 average map value = 0.00327, steps = 452 
    6261 shifted from previous position = 75.9 
    6262 rotated from previous position = 42.1 degrees 
    6263 atoms outside contour = 24361, contour level = 0.0074163 
    6264  
    6265 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6266 Matrix rotation and translation 
    6267 -0.84320714 -0.43778965 -0.31199677 814.71784677 
    6268 0.25219295 -0.83466991 0.48961711 413.52774321 
    6269 -0.47476360 0.33416525 0.81420706 189.19622244 
    6270 Axis -0.21419046 0.22426945 0.95069746 
    6271 Axis point 389.99195147 267.01204412 0.00000000 
    6272 Rotation angle (degrees) 158.72268536 
    6273 Shift along axis 98.10521687 
    6274  
    6275 
    6276 > view matrix models
    6277 > #11,-0.83539,-0.46224,-0.29741,734.38,0.27698,-0.82138,0.49862,344.68,-0.47476,0.33417,0.81421,189.82
    6278 
    6279 > fitmap #11 inMap #3
    6280 
    6281 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6282 average map value = 0.003241, steps = 300 
    6283 shifted from previous position = 30.1 
    6284 rotated from previous position = 23.8 degrees 
    6285 atoms outside contour = 24235, contour level = 0.0074163 
    6286  
    6287 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6288 Matrix rotation and translation 
    6289 -0.91147793 -0.05187608 -0.40806481 731.10046280 
    6290 -0.06537740 -0.96113746 0.26821749 597.31034546 
    6291 -0.40612044 0.27115253 0.87266404 158.90685757 
    6292 Axis 0.21035502 -0.13935337 -0.96764219 
    6293 Axis point 383.87827230 285.86350157 0.00000000 
    6294 Rotation angle (degrees) 179.60027832 
    6295 Shift along axis -83.21153398 
    6296  
    6297 
    6298 > fitmap #11 inMap #3
    6299 
    6300 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6301 average map value = 0.003241, steps = 44 
    6302 shifted from previous position = 0.00647 
    6303 rotated from previous position = 0.00353 degrees 
    6304 atoms outside contour = 24236, contour level = 0.0074163 
    6305  
    6306 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6307 Matrix rotation and translation 
    6308 -0.91149066 -0.05186828 -0.40803738 731.09314216 
    6309 -0.06535521 -0.96115182 0.26817143 597.32073157 
    6310 -0.40609546 0.27110311 0.87269102 158.90535884 
    6311 Axis 0.21033996 -0.13932770 -0.96764916 
    6312 Axis point 383.87197070 285.87246651 0.00000000 
    6313 Rotation angle (degrees) 179.60070718 
    6314 Shift along axis -83.20985401 
    6315  
    6316 
    6317 > ui mousemode right "rotate selected models"
    6318 
    6319 > view matrix models
    6320 > #11,-0.93785,-0.34691,0.009644,657.66,0.34313,-0.93107,-0.12401,564.89,0.052,-0.11299,0.99223,-5.8209
    6321 
    6322 > view matrix models
    6323 > #11,-0.88937,-0.45211,0.067899,638.07,0.45237,-0.89174,-0.01236,472.75,0.066136,0.019723,0.99762,-39.905
    6324 
    6325 > view matrix models
    6326 > #11,-0.75515,-0.29587,0.58498,369.72,0.26703,-0.9538,-0.13769,605.6,0.5987,0.05223,0.79927,-196.15
    6327 
    6328 > fitmap #11 inMap #3
    6329 
    6330 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6331 average map value = 0.00341, steps = 128 
    6332 shifted from previous position = 17.9 
    6333 rotated from previous position = 5.64 degrees 
    6334 atoms outside contour = 23850, contour level = 0.0074163 
    6335  
    6336 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6337 Matrix rotation and translation 
    6338 -0.79425260 -0.30803534 0.52371469 423.32573853 
    6339 0.30338390 -0.94787616 -0.09741164 564.42851116 
    6340 0.52642289 0.08151715 0.84630605 -179.54895904 
    6341 Axis 0.28086269 -0.00425103 0.95973855 
    6342 Axis point 189.86976609 319.21672061 0.00000000 
    6343 Rotation angle (degrees) 161.42569310 
    6344 Shift along axis -55.82305646 
    6345  
    6346 
    6347 > fitmap #11 inMap #3
    6348 
    6349 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6350 average map value = 0.00341, steps = 76 
    6351 shifted from previous position = 0.0195 
    6352 rotated from previous position = 0.0111 degrees 
    6353 atoms outside contour = 23837, contour level = 0.0074163 
    6354  
    6355 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6356 Matrix rotation and translation 
    6357 -0.79423679 -0.30816124 0.52366458 423.38085284 
    6358 0.30341461 -0.94784752 -0.09759458 564.46534613 
    6359 0.52642903 0.08137427 0.84631598 -179.50859711 
    6360 Axis 0.28085424 -0.00433822 0.95974063 
    6361 Axis point 189.87507217 319.24164873 0.00000000 
    6362 Rotation angle (degrees) 161.42080325 
    6363 Shift along axis -55.82216337 
    6364  
    6365 
    6366 > combine #8
    6367 
    6368 > ui mousemode right "translate selected models"
    6369 
    6370 > view matrix models
    6371 > #11,-0.78493,-0.33601,0.52055,713.52,0.32673,-0.93834,-0.11301,476.56,0.52643,0.081374,0.84632,-207.08
    6372 
    6373 > view matrix models
    6374 > #11,-0.78493,-0.33601,0.52055,693.7,0.32673,-0.93834,-0.11301,533.75,0.52643,0.081374,0.84632,-221.57
    6375 
    6376 > view matrix models
    6377 > #11,-0.78493,-0.33601,0.52055,705.44,0.32673,-0.93834,-0.11301,541.84,0.52643,0.081374,0.84632,-231.41
    6378 
    6379 > fitmap #12 inMap #3
    6380 
    6381 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6382 average map value = 0.007156, steps = 60 
    6383 shifted from previous position = 0.0162 
    6384 rotated from previous position = 0.00835 degrees 
    6385 atoms outside contour = 16472, contour level = 0.0074163 
    6386  
    6387 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6388 Matrix rotation and translation 
    6389 -0.99158996 -0.12941319 -0.00126807 791.16940967 
    6390 0.12903227 -0.98781901 -0.08697311 715.07330059 
    6391 0.01000285 -0.08640529 0.99620987 15.46353863 
    6392 Axis 0.00219496 -0.04356891 0.99904801 
    6393 Axis point 372.34489862 383.59084787 0.00000000 
    6394 Rotation angle (degrees) 172.56820583 
    6395 Shift along axis -13.96956072 
    6396  
    6397 
    6398 > fitmap #12 inMap #3
    6399 
    6400 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6401 average map value = 0.007155, steps = 100 
    6402 shifted from previous position = 0.0188 
    6403 rotated from previous position = 0.0091 degrees 
    6404 atoms outside contour = 16462, contour level = 0.0074163 
    6405  
    6406 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6407 Matrix rotation and translation 
    6408 -0.99158484 -0.12945084 -0.00141814 791.23356076 
    6409 0.12908240 -0.98780932 -0.08700878 715.06127156 
    6410 0.00986251 -0.08645965 0.99620655 15.55431667 
    6411 Axis 0.00212199 -0.04359169 0.99904718 
    6412 Axis point 372.36982684 383.59789292 0.00000000 
    6413 Rotation angle (degrees) 172.56566143 
    6414 Shift along axis -13.95224264 
    6415  
    6416 
    6417 > view matrix models
    6418 > #11,-0.78493,-0.33601,0.52055,699.86,0.32673,-0.93834,-0.11301,542.95,0.52643,0.081374,0.84632,-199.4
    6419 
    6420 > view matrix models
    6421 > #11,-0.78493,-0.33601,0.52055,714.99,0.32673,-0.93834,-0.11301,528.78,0.52643,0.081374,0.84632,-201.15
    6422 
    6423 > ui mousemode right "rotate selected models"
    6424 
    6425 > view matrix models
    6426 > #11,-0.80067,-0.59659,-0.054814,975.71,0.52077,-0.73829,0.42863,218.43,-0.29618,0.31464,0.90182,72.16
    6427 
    6428 > fitmap #12 inMap #3
    6429 
    6430 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6431 average map value = 0.007155, steps = 64 
    6432 shifted from previous position = 0.013 
    6433 rotated from previous position = 0.00603 degrees 
    6434 atoms outside contour = 16460, contour level = 0.0074163 
    6435  
    6436 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6437 Matrix rotation and translation 
    6438 -0.99158487 -0.12945173 -0.00131830 791.19487858 
    6439 0.12907498 -0.98781320 -0.08697565 715.04266904 
    6440 0.00995692 -0.08641390 0.99620958 15.50296632 
    6441 Axis 0.00217081 -0.04357183 0.99904794 
    6442 Axis point 372.35138150 383.58538653 0.00000000 
    6443 Rotation angle (degrees) 172.56585596 
    6444 Shift along axis -13.94998169 
    6445  
    6446 
    6447 > fitmap #12 inMap #3
    6448 
    6449 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6450 average map value = 0.007156, steps = 48 
    6451 shifted from previous position = 0.0242 
    6452 rotated from previous position = 0.0126 degrees 
    6453 atoms outside contour = 16475, contour level = 0.0074163 
    6454  
    6455 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6456 Matrix rotation and translation 
    6457 -0.99159194 -0.12939924 -0.00113738 791.11387296 
    6458 0.12900820 -0.98783180 -0.08686348 715.04301724 
    6459 0.01011653 -0.08627986 0.99621959 15.37902198 
    6460 Axis 0.00225636 -0.04350968 0.99905046 
    6461 Axis point 372.32125683 383.56768677 0.00000000 
    6462 Rotation angle (degrees) 172.56932375 
    6463 Shift along axis -13.96183465 
    6464  
    6465 
    6466 > ui mousemode right "rotate selected models"
    6467 
    6468 > ui mousemode right "translate selected models"
    6469 
    6470 > view matrix models
    6471 > #11,-0.80067,-0.59659,-0.054814,975.98,0.52077,-0.73829,0.42863,245.53,-0.29618,0.31464,0.90182,70.489
    6472 
    6473 > fitmap #12 inMap #3
    6474 
    6475 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6476 average map value = 0.007155, steps = 84 
    6477 shifted from previous position = 0.0229 
    6478 rotated from previous position = 0.0192 degrees 
    6479 atoms outside contour = 16465, contour level = 0.0074163 
    6480  
    6481 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6482 Matrix rotation and translation 
    6483 -0.99158539 -0.12944658 -0.00142738 791.21930989 
    6484 0.12907882 -0.98780857 -0.08702257 715.05883655 
    6485 0.00985479 -0.08647456 0.99620534 15.56413078 
    6486 Axis 0.00211773 -0.04359891 0.99904687 
    6487 Axis point 372.36350064 383.59570975 0.00000000 
    6488 Rotation angle (degrees) 172.56588578 
    6489 Shift along axis -13.95090046 
    6490  
    6491 
    6492 > fitmap #12 inMap #3
    6493 
    6494 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6495 average map value = 0.007155, steps = 120 
    6496 shifted from previous position = 0.00997 
    6497 rotated from previous position = 0.00417 degrees 
    6498 atoms outside contour = 16461, contour level = 0.0074163 
    6499  
    6500 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6501 Matrix rotation and translation 
    6502 -0.99158290 -0.12946627 -0.00136553 791.21122951 
    6503 0.12909340 -0.98780953 -0.08699002 715.04031812 
    6504 0.00991340 -0.08643410 0.99620827 15.52434575 
    6505 Axis 0.00214800 -0.04358058 0.99904761 
    6506 Axis point 372.35679290 383.58859204 0.00000000 
    6507 Rotation angle (degrees) 172.56490025 
    6508 Shift along axis -13.95278770 
    6509  
    6510 
    6511 > ui mousemode right "rotate selected models"
    6512 
    6513 > view matrix models
    6514 > #11,-0.59669,-0.80204,-0.026407,922.68,0.80245,-0.59613,-0.026482,261.31,0.005497,-0.036992,0.9993,-18.361
    6515 
    6516 > ui mousemode right "translate selected models"
    6517 
    6518 > view matrix models
    6519 > #11,-0.59669,-0.80204,-0.026407,918.9,0.80245,-0.59613,-0.026482,245.43,0.005497,-0.036992,0.9993,-16.915
    6520 
    6521 > fitmap #12 inMap #3
    6522 
    6523 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6524 average map value = 0.007156, steps = 64 
    6525 shifted from previous position = 0.0242 
    6526 rotated from previous position = 0.0168 degrees 
    6527 atoms outside contour = 16476, contour level = 0.0074163 
    6528  
    6529 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6530 Matrix rotation and translation 
    6531 -0.99159516 -0.12937502 -0.00108988 791.08922604 
    6532 0.12897830 -0.98782129 -0.08702722 715.11785477 
    6533 0.01018255 -0.08643634 0.99620536 15.39738426 
    6534 Axis 0.00228489 -0.04359023 0.99904688 
    6535 Axis point 372.31106342 383.60009482 0.00000000 
    6536 Rotation angle (degrees) 172.57086216 
    6537 Shift along axis -13.98188736 
    6538  
    6539 
    6540 > fitmap #11 inMap #3
    6541 
    6542 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6543 average map value = 0.007129, steps = 144 
    6544 shifted from previous position = 13.4 
    6545 rotated from previous position = 7.72 degrees 
    6546 atoms outside contour = 16510, contour level = 0.0074163 
    6547  
    6548 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6549 Matrix rotation and translation 
    6550 -0.51770630 -0.85277811 -0.06891806 915.69536645 
    6551 0.85549986 -0.51504609 -0.05336246 218.45088712 
    6552 0.01001036 -0.08658547 0.99619415 15.53328191 
    6553 Axis -0.01942386 -0.04614555 0.99874586 
    6554 Axis point 396.55805348 367.73548446 0.00000000 
    6555 Rotation angle (degrees) 121.21688865 
    6556 Shift along axis -12.35307371 
    6557  
    6558 
    6559 > fitmap #8 inMap #3
    6560 
    6561 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    6562 average map value = 0.007156, steps = 60 
    6563 shifted from previous position = 0.0162 
    6564 rotated from previous position = 0.00835 degrees 
    6565 atoms outside contour = 16472, contour level = 0.0074163 
    6566  
    6567 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    6568 Matrix rotation and translation 
    6569 -0.99158996 -0.12941319 -0.00126807 791.16940967 
    6570 0.12903227 -0.98781901 -0.08697311 715.07330059 
    6571 0.01000285 -0.08640529 0.99620987 15.46353863 
    6572 Axis 0.00219496 -0.04356891 0.99904801 
    6573 Axis point 372.34489862 383.59084787 0.00000000 
    6574 Rotation angle (degrees) 172.56820583 
    6575 Shift along axis -13.96956072 
    6576  
    6577 
    6578 > fitmap #9 inMap #3
    6579 
    6580 Fit molecule copy of 8i8b (#9) to map emd_51808.map (#3) using 30015 atoms 
    6581 average map value = 0.007136, steps = 48 
    6582 shifted from previous position = 0.0295 
    6583 rotated from previous position = 0.0195 degrees 
    6584 atoms outside contour = 16528, contour level = 0.0074163 
    6585  
    6586 Position of copy of 8i8b (#9) relative to emd_51808.map (#3) coordinates: 
    6587 Matrix rotation and translation 
    6588 -0.94922563 0.31243064 0.03684897 582.13275372 
    6589 -0.31443114 -0.94599050 -0.07896236 874.70117765 
    6590 0.01018851 -0.08653957 0.99619633 15.42358187 
    6591 Axis -0.01207572 0.04248852 -0.99902397 
    6592 Axis point 361.37491136 390.77680339 0.00000000 
    6593 Rotation angle (degrees) 161.71540948 
    6594 Shift along axis 14.72655921 
    6595  
    6596 
    6597 > fitmap #10 inMap #3
    6598 
    6599 Fit molecule copy of 8i8b (#10) to map emd_51808.map (#3) using 30015 atoms 
    6600 average map value = 0.007155, steps = 80 
    6601 shifted from previous position = 0.0228 
    6602 rotated from previous position = 0.0152 degrees 
    6603 atoms outside contour = 16464, contour level = 0.0074163 
    6604  
    6605 Position of copy of 8i8b (#10) relative to emd_51808.map (#3) coordinates: 
    6606 Matrix rotation and translation 
    6607 -0.83743571 -0.54515231 -0.03886406 910.07080810 
    6608 0.54644204 -0.83385467 -0.07802261 480.95563280 
    6609 0.01012723 -0.08657588 0.99619380 15.46315078 
    6610 Axis -0.00782746 -0.04483398 0.99896379 
    6611 Axis point 383.60821954 376.24666945 0.00000000 
    6612 Rotation angle (degrees) 146.88212261 
    6613 Shift along axis -13.23957343 
    6614  
    6615 
    6616 > fitmap #11 inMap #3
    6617 
    6618 Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms 
    6619 average map value = 0.00713, steps = 64 
    6620 shifted from previous position = 0.0276 
    6621 rotated from previous position = 0.0114 degrees 
    6622 atoms outside contour = 16526, contour level = 0.0074163 
    6623  
    6624 Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates: 
    6625 Matrix rotation and translation 
    6626 -0.51764871 -0.85279984 -0.06908158 915.74510300 
    6627 0.85553660 -0.51499520 -0.05326455 218.38344752 
    6628 0.00984732 -0.08667415 0.99618806 15.60319362 
    6629 Axis -0.01953224 -0.04614416 0.99874382 
    6630 Axis point 396.59938666 367.73547110 0.00000000 
    6631 Rotation angle (degrees) 121.21345848 
    6632 Shift along axis -12.38007902 
    6633  
    6634 
    6635 > fitmap #12 inMap #3
    6636 
    6637 Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms 
    6638 average map value = 0.007155, steps = 76 
    6639 shifted from previous position = 0.0235 
    6640 rotated from previous position = 0.0207 degrees 
    6641 atoms outside contour = 16463, contour level = 0.0074163 
    6642  
    6643 Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates: 
    6644 Matrix rotation and translation 
    6645 -0.99158394 -0.12945761 -0.00143107 791.22700647 
    6646 0.12909091 -0.98781408 -0.08694202 715.02758127 
    6647 0.00984168 -0.08639506 0.99621236 15.54686751 
    6648 Axis 0.00211351 -0.04355865 0.99904864 
    6649 Axis point 372.36637181 383.58186833 0.00000000 
    6650 Rotation angle (degrees) 172.56523034 
    6651 Shift along axis -13.94129314 
    6652  
    6653 
    6654 > view front
    6655 
    6656 > combine #8
    6657 
    6658 > select subtract #11
    6659 
    6660 Nothing selected 
    6661 
    6662 > select add #13
    6663 
    6664 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6665 
    6666 > view matrix models
    6667 > #13,-0.98735,-0.15852,-0.003891,655.72,0.15825,-0.98356,-0.087032,724.5,0.009969,-0.086547,0.9962,15.553
    6668 
    6669 > view matrix models
    6670 > #13,-0.98735,-0.15852,-0.003891,640.23,0.15825,-0.98356,-0.087032,647.89,0.009969,-0.086547,0.9962,47.543
    6671 
    6672 > fitmap #13 inMap #3
    6673 
    6674 Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms 
    6675 average map value = 0.003621, steps = 260 
    6676 shifted from previous position = 39.3 
    6677 rotated from previous position = 15.8 degrees 
    6678 atoms outside contour = 23329, contour level = 0.0074163 
    6679  
    6680 Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates: 
    6681 Matrix rotation and translation 
    6682 -0.97326751 -0.18416075 -0.13724144 707.66029233 
    6683 0.16366317 -0.97533150 0.14813128 539.23991406 
    6684 -0.16113586 0.12170998 0.97939877 65.44032184 
    6685 Axis -0.07556641 0.06833941 0.99479618 
    6686 Axis point 332.58747192 298.86600265 0.00000000 
    6687 Rotation angle (degrees) 169.93171792 
    6688 Shift along axis 48.47577371 
    6689  
    6690 
    6691 > view matrix models
    6692 > #13,-0.96801,-0.21288,-0.13281,683.19,0.19233,-0.96947,0.15212,518.26,-0.16114,0.12171,0.9794,42.533
    6693 
    6694 > fitmap #13 inMap #3
    6695 
    6696 Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms 
    6697 average map value = 0.003621, steps = 260 
    6698 shifted from previous position = 34.4 
    6699 rotated from previous position = 0.00485 degrees 
    6700 atoms outside contour = 23329, contour level = 0.0074163 
    6701  
    6702 Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates: 
    6703 Matrix rotation and translation 
    6704 -0.97328676 -0.18410047 -0.13718574 707.63652673 
    6705 0.16361206 -0.97534226 0.14811691 539.26776651 
    6706 -0.16107144 0.12171498 0.97940875 65.40965565 
    6707 Axis -0.07553541 0.06833652 0.99479873 
    6708 Axis point 332.57998105 298.86953806 0.00000000 
    6709 Rotation angle (degrees) 169.93500175 
    6710 Shift along axis 48.46950495 
    6711  
    6712 
    6713 > view matrix models
    6714 > #13,-0.96803,-0.21282,-0.13275,679.51,0.19228,-0.96948,0.1521,547.92,-0.16107,0.12171,0.97941,59.759
    6715 
    6716 > ui mousemode right "rotate selected models"
    6717 
    6718 > view matrix models
    6719 > #13,-0.43132,-0.53774,0.72443,221.1,0.61779,-0.76121,-0.19722,454.04,0.6575,0.36248,0.66053,-213.36
    6720 
    6721 > ui mousemode right "translate selected models"
    6722 
    6723 > view matrix models
    6724 > #13,-0.43132,-0.53774,0.72443,248.04,0.61779,-0.76121,-0.19722,442.55,0.6575,0.36248,0.66053,-218.86
    6725 
    6726 > fitmap #13 inMap #3
    6727 
    6728 Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms 
    6729 average map value = 0.00325, steps = 204 
    6730 shifted from previous position = 33.7 
    6731 rotated from previous position = 24.7 degrees 
    6732 atoms outside contour = 23928, contour level = 0.0074163 
    6733  
    6734 Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates: 
    6735 Matrix rotation and translation 
    6736 -0.77856351 -0.32137393 0.53903403 417.70671143 
    6737 0.39075391 -0.92036183 0.01566958 478.95755449 
    6738 0.49107054 0.22282940 0.84213824 -184.48301526 
    6739 Axis 0.27874148 0.06453671 0.95819528 
    6740 Axis point 187.33514674 288.51786812 0.00000000 
    6741 Rotation angle (degrees) 158.18576626 
    6742 Shift along axis -29.42822342 
    6743  
    6744 
    6745 > view matrix models
    6746 > #13,-0.76669,-0.34841,0.53926,399.38,0.41357,-0.91047,-0.00025197,494.87,0.49107,0.22283,0.84214,-195.41
    6747 
    6748 > ui mousemode right "rotate selected models"
    6749 
    6750 > view matrix models
    6751 > #13,-0.91927,0.16249,0.35854,424.42,-0.16587,-0.98591,0.021529,741.11,0.35698,-0.03968,0.93327,-120.05
    6752 
    6753 > fitmap #13 inMap #3
    6754 
    6755 Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms 
    6756 average map value = 0.007127, steps = 300 
    6757 shifted from previous position = 22.8 
    6758 rotated from previous position = 37.6 degrees 
    6759 atoms outside contour = 16529, contour level = 0.0074163 
    6760  
    6761 Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates: 
    6762 Matrix rotation and translation 
    6763 -0.71883894 0.69190206 0.06739559 324.88314871 
    6764 -0.69510441 -0.71677641 -0.05533054 927.69885470 
    6765 0.01002426 -0.08662072 0.99619095 15.53148650 
    6766 Axis -0.02253451 0.04131758 -0.99889191 
    6767 Axis point 349.60742573 398.44733584 0.00000000 
    6768 Rotation angle (degrees) 136.03072354 
    6769 Shift along axis 15.49491660 
    6770  
    6771 
    6772 > fitmap #13 inMap #3
    6773 
    6774 Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms 
    6775 average map value = 0.007127, steps = 64 
    6776 shifted from previous position = 0.021 
    6777 rotated from previous position = 0.0119 degrees 
    6778 atoms outside contour = 16536, contour level = 0.0074163 
    6779  
    6780 Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates: 
    6781 Matrix rotation and translation 
    6782 -0.71880030 0.69193509 0.06746860 324.83218556 
    6783 -0.69514172 -0.71675497 -0.05513918 927.65237469 
    6784 0.01020572 -0.08653430 0.99619662 15.41227467 
    6785 Axis -0.02260897 0.04123745 -0.99889354 
    6786 Axis point 349.58587803 398.42661262 0.00000000 
    6787 Rotation angle (degrees) 136.02801080 
    6788 Shift along axis 15.51467650 
    6789  
    6790 
    6791 > combine #8
    6792 
    6793 > select subtract #13
    6794 
    6795 Nothing selected 
    6796 
    6797 > select add #14
    6798 
    6799 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6800 
    6801 > view matrix models
    6802 > #14,-0.15337,-0.97947,0.13083,573.92,0.95957,-0.17924,-0.21702,257.15,0.23602,0.09226,0.96736,-113.11
    6803 
    6804 > ui mousemode right "move picked models"
    6805 
    6806 > ui mousemode right "translate selected models"
    6807 
    6808 > view matrix models
    6809 > #14,-0.15337,-0.97947,0.13083,788.32,0.95957,-0.17924,-0.21702,181,0.23602,0.09226,0.96736,-72.466
    6810 
    6811 > view matrix models
    6812 > #14,-0.15337,-0.97947,0.13083,758.58,0.95957,-0.17924,-0.21702,69.828,0.23602,0.09226,0.96736,-75.68
    6813 
    6814 > fitmap #14 inMap #3
    6815 
    6816 Fit molecule copy of 8i8b (#14) to map emd_51808.map (#3) using 30015 atoms 
    6817 average map value = 0.007107, steps = 276 
    6818 shifted from previous position = 48.3 
    6819 rotated from previous position = 17.9 degrees 
    6820 atoms outside contour = 16591, contour level = 0.0074163 
    6821  
    6822 Position of copy of 8i8b (#14) relative to emd_51808.map (#3) coordinates: 
    6823 Matrix rotation and translation 
    6824 -0.09518255 -0.99180092 -0.08527172 806.75837585 
    6825 0.99540916 -0.09396336 -0.01820812 -20.63958015 
    6826 0.01004642 -0.08661335 0.99619138 15.51851676 
    6827 Axis -0.03436291 -0.04788243 0.99826172 
    6828 Axis point 413.27522164 356.68473371 0.00000000 
    6829 Rotation angle (degrees) 95.53635131 
    6830 Shift along axis -11.24275285 
    6831  
    6832 
    6833 > fitmap #14 inMap #3
    6834 
    6835 Fit molecule copy of 8i8b (#14) to map emd_51808.map (#3) using 30015 atoms 
    6836 average map value = 0.007107, steps = 104 
    6837 shifted from previous position = 0.00975 
    6838 rotated from previous position = 0.0135 degrees 
    6839 atoms outside contour = 16591, contour level = 0.0074163 
    6840  
    6841 Position of copy of 8i8b (#14) relative to emd_51808.map (#3) coordinates: 
    6842 Matrix rotation and translation 
    6843 -0.09510822 -0.99180556 -0.08530066 806.73582245 
    6844 0.99541849 -0.09390815 -0.01798183 -20.73986080 
    6845 0.00982406 -0.08662008 0.99619301 15.61922924 
    6846 Axis -0.03447975 -0.04778496 0.99826236 
    6847 Axis point 413.31210875 356.64958440 0.00000000 
    6848 Rotation angle (degrees) 95.53257599 
    6849 Shift along axis -11.23290641 
    6850  
    6851 
    6852 > view front
    6853 
    6854 > select clear
    6855 
    6856 > combine #8
    6857 
    6858 > select add #15
    6859 
    6860 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    6861 
    6862 > view matrix models
    6863 > #15,-0.98735,-0.15852,-0.003891,591.43,0.15825,-0.98356,-0.087032,569.81,0.009969,-0.086547,0.9962,-23.671
    6864 
    6865 > ui mousemode right "rotate selected models"
    6866 
    6867 > view matrix models
    6868 > #15,-0.72794,-0.64063,0.24434,492.87,0.62804,-0.76598,-0.13723,350.55,0.27508,0.053559,0.95993,-148.05
    6869 
    6870 > view matrix models
    6871 > #15,-0.77289,-0.51176,0.37515,439.78,0.24756,-0.78756,-0.56433,662.02,0.58425,-0.34329,0.73539,-117.68
    6872 
    6873 > view matrix models
    6874 > #15,-0.47576,-0.36838,0.79871,139.73,0.052442,-0.91833,-0.39232,707.91,0.87801,-0.14476,0.45623,-179.99
    6875 
    6876 > ui mousemode right "translate selected models"
    6877 
    6878 > view matrix models
    6879 > #15,-0.47576,-0.36838,0.79871,155.35,0.052442,-0.91833,-0.39232,703.72,0.87801,-0.14476,0.45623,-145.5
    6880 
    6881 > ui mousemode right "rotate selected models"
    6882 
    6883 > view matrix models
    6884 > #15,-0.34277,0.12528,0.93103,-44.102,0.27709,-0.93349,0.22763,395.94,0.89762,0.33601,0.28526,-188.91
    6885 
    6886 > view matrix models
    6887 > #15,-0.10038,-0.33683,0.9362,-54.078,0.83305,-0.54294,-0.10602,206.55,0.54401,0.76926,0.33509,-146.71
    6888 
    6889 > fitmap #15 inMap #3
    6890 
    6891 Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms 
    6892 average map value = 0.002648, steps = 252 
    6893 shifted from previous position = 41.8 
    6894 rotated from previous position = 22.9 degrees 
    6895 atoms outside contour = 25287, contour level = 0.0074163 
    6896  
    6897 Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates: 
    6898 Matrix rotation and translation 
    6899 -0.45511012 -0.33626603 0.82449983 156.80799843 
    6900 0.82909803 -0.49774687 0.25464596 71.53569237 
    6901 0.32476342 0.79948312 0.50532712 -141.08499453 
    6902 Axis 0.39478286 0.36210337 0.84440964 
    6903 Axis point 91.73905266 106.11892433 -0.00000000 
    6904 Rotation angle (degrees) 136.36620084 
    6905 Shift along axis -31.32510508 
    6906  
    6907 
    6908 > view matrix models
    6909 > #15,0.8708,-0.16948,0.46151,-293.25,0.45854,0.61857,-0.63805,320.99,-0.17734,0.76723,0.61636,23.204
    6910 
    6911 > ui mousemode right "translate selected models"
    6912 
    6913 > view matrix models
    6914 > #15,0.8708,-0.16948,0.46151,-336.97,0.45854,0.61857,-0.63805,303.66,-0.17734,0.76723,0.61636,49.165
    6915 
    6916 > fitmap #15 inMap #3
    6917 
    6918 Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms 
    6919 average map value = 0.003506, steps = 432 
    6920 shifted from previous position = 65.9 
    6921 rotated from previous position = 30.8 degrees 
    6922 atoms outside contour = 24105, contour level = 0.0074163 
    6923  
    6924 Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates: 
    6925 Matrix rotation and translation 
    6926 0.97535722 -0.18376330 0.12210397 -216.16414053 
    6927 0.21792335 0.88884732 -0.40306314 255.84314316 
    6928 -0.03446358 0.41973983 0.90698995 -55.63716744 
    6929 Axis 0.88577434 0.16855009 0.43242883 
    6930 Axis point 0.00000000 105.13499396 677.85095327 
    6931 Rotation angle (degrees) 27.67489445 
    6932 Shift along axis -172.40937870 
    6933  
    6934 
    6935 > fitmap #15 inMap #3
    6936 
    6937 Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms 
    6938 average map value = 0.003506, steps = 40 
    6939 shifted from previous position = 0.00515 
    6940 rotated from previous position = 0.00876 degrees 
    6941 atoms outside contour = 24113, contour level = 0.0074163 
    6942  
    6943 Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates: 
    6944 Matrix rotation and translation 
    6945 0.97535280 -0.18378837 0.12210159 -216.15304239 
    6946 0.21793990 0.88890645 -0.40292376 255.77732346 
    6947 -0.03448419 0.41960361 0.90705219 -55.61223151 
    6948 Axis 0.88569030 0.16861020 0.43257749 
    6949 Axis point 0.00000000 105.01301844 677.98228811 
    6950 Rotation angle (degrees) 27.66768014 
    6951 Shift along axis -172.37458845 
    6952  
    6953 
    6954 > ui mousemode right "rotate selected models"
    6955 
    6956 > view matrix models
    6957 > #15,-0.72151,0.57752,0.38196,242.16,-0.68073,-0.69252,-0.23879,886.94,0.12661,-0.4323,0.8928,42.128
    6958 
    6959 > ui mousemode right "translate selected models"
    6960 
    6961 > view matrix models
    6962 > #15,-0.72151,0.57752,0.38196,179.19,-0.68073,-0.69252,-0.23879,892.73,0.12661,-0.4323,0.8928,71.955
    6963 
    6964 > view matrix models
    6965 > #15,-0.72151,0.57752,0.38196,195,-0.68073,-0.69252,-0.23879,911.17,0.12661,-0.4323,0.8928,77.246
    6966 
    6967 > fitmap #15 inMap #3
    6968 
    6969 Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms 
    6970 average map value = 0.007109, steps = 268 
    6971 shifted from previous position = 22.7 
    6972 rotated from previous position = 34 degrees 
    6973 atoms outside contour = 16612, contour level = 0.0074163 
    6974  
    6975 Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates: 
    6976 Matrix rotation and translation 
    6977 -0.34626017 0.93430523 0.08472110 70.16210393 
    6978 -0.93808526 -0.34578823 -0.02065362 863.81775833 
    6979 0.00999878 -0.08662715 0.99619064 15.52638035 
    6980 Axis -0.03518510 0.03985102 -0.99858595 
    6981 Axis point 335.40888064 407.58273783 0.00000000 
    6982 Rotation angle (degrees) 110.36068810 
    6983 Shift along axis 16.45092923 
    6984  
    6985 
    6986 > fitmap #15 inMap #3
    6987 
    6988 Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms 
    6989 average map value = 0.007109, steps = 60 
    6990 shifted from previous position = 0.0201 
    6991 rotated from previous position = 0.0103 degrees 
    6992 atoms outside contour = 16596, contour level = 0.0074163 
    6993  
    6994 Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates: 
    6995 Matrix rotation and translation 
    6996 -0.34620781 0.93430916 0.08489165 70.08290633 
    6997 -0.93810372 -0.34573984 -0.02062536 863.79841473 
    6998 0.01007997 -0.08677784 0.99617671 15.55204246 
    6999 Axis -0.03527993 0.03989799 -0.99858073 
    7000 Axis point 335.37735797 407.59951129 0.00000000 
    7001 Rotation angle (degrees) 110.35803510 
    7002 Shift along axis 16.46132973 
    7003  
    7004 
    7005 > view front
    7006 
    7007 > select clear
    7008 
    7009 > vop copy #3
    7010 
    7011 Opened emd_51808.map copy as #16, grid size 500,500,500, pixel 1.35, shown at
    7012 step 1, values float32 
    7013 
    7014 > close #16
    7015 
    7016 > show #!3 models
    7017 
    7018 > volume zone #3 nearAtoms #8/A-C newMap true
    7019 
    7020 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    7021 step 1, values float32 
    7022 
    7023 > volume zone #3 nearAtoms #8-15/A-C newMap true
    7024 
    7025 Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
    7026 step 1, values float32 
    7027 
    7028 > close #16
    7029 
    7030 > volume zone #3 nearAtoms #8-15/A-C range 4 newMap true
    7031 
    7032 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    7033 step 1, values float32 
    7034 
    7035 > hide #!16 models
    7036 
    7037 > show #!16 models
    7038 
    7039 > hide #!16 models
    7040 
    7041 > volume #17 level 0.006533
    7042 
    7043 > show #!16 models
    7044 
    7045 > hide #!17 models
    7046 
    7047 > show #!17 models
    7048 
    7049 > hide #!16 models
    7050 
    7051 > close #16
    7052 
    7053 > close #17
    7054 
    7055 > volume zone #3 nearAtoms #8-15/A-C newMap true
    7056 
    7057 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    7058 step 1, values float32 
    7059 
    7060 > volume zone #3 nearAtoms #8-15/A-C invert true newMap true
    7061 
    7062 Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
    7063 step 1, values float32 
    7064 
    7065 > color #16 #b9c2ffff models
    7066 
    7067 > color #17 #b9c2ffff models
    7068 
    7069 > hide #!16 models
    7070 
    7071 > show #!16 models
    7072 
    7073 > transparency #16 70
    7074 
    7075 > transparency #16 65
    7076 
    7077 > transparency #16 50
    7078 
    7079 > color #16 #dbd3beff models
    7080 
    7081 > color #16 #dbd3be7f models
    7082 
    7083 > color #16 #dfd9fcff models
    7084 
    7085 > color #16 #dfd9fc7c models
    7086 
    7087 > color #16 #d2d2d3ff models
    7088 
    7089 > color #16 #d2d2d380 models
    7090 
    7091 > color #16 #d2d2d391 models
    7092 
    7093 > volume #16 level 0.007053
    7094 
    7095 > hide #!8 models
    7096 
    7097 > show #!8 models
    7098 
    7099 > hide #!8 models
    7100 
    7101 > show #!8 models
    7102 
    7103 > hide #!9 models
    7104 
    7105 > show #!9 models
    7106 
    7107 > hide #!9 models
    7108 
    7109 > show #!9 models
    7110 
    7111 > color #16 #ff91aaff models
    7112 
    7113 > color #16 #ff91aa4f models
    7114 
    7115 > color #16 #ff91aa5f models
    7116 
    7117 > hide #!16 models
    7118 
    7119 > show #!16 models
    7120 
    7121 > hide #!17 models
    7122 
    7123 > show #!17 models
    7124 
    7125 > view front
    7126 
    7127 > color #16 #0000005f models
    7128 
    7129 > color #16 #ff92ad5f models
    7130 
    7131 > color #16 #ff92adab models
    7132 
    7133 > color #16 #ff92ad76 models
    7134 
    7135 > color #16 #ffd7e076 models
    7136 
    7137 > color #16 #b9c2ffff models
    7138 
    7139 > color #16 #b9c2ff80 models
    7140 
    7141 > color #16 #b9c2ff72 models
    7142 
    7143 > color #16 #b9c2ffff models
    7144 
    7145 > color #16 #b9c2fff4 models
    7146 
    7147 > color #16 #b9c2ff5c models
    7148 
    7149 > color #16 #fafff15c models
    7150 
    7151 > color #16 #fafff185 models
    7152 
    7153 > color #16 #fafff154 models
    7154 
    7155 > color #16 #ff91aaff models
    7156 
    7157 > color #16 #ff91aa80 models
    7158 
    7159 > view front
    7160 
    7161 > ui tool show "Hide Dust"
    7162 
    7163 > surface dust #2 size 1.35
    7164 
    7165 > surface dust #17 size 8.1
    7166 
    7167 > surface dust #17 size 7.5
    7168 
    7169 > surface dust #17 size 21.62
    7170 
    7171 > surface dust #2 size 1.44
    7172 
    7173 > surface dust #2 size 6.66
    7174 
    7175 > surface dust #7 size 8.43
    7176 
    7177 > surface dust #7 size 10.15
    7178 
    7179 > view front
    7180 
    7181 > lighting gentle
    7182 
    7183 > lighting soft
    7184 
    7185 > lighting gentle
    7186 
    7187 > lighting soft
    7188 
    7189 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    7190 
    7191 ——— End of log from Sun Jun 15 21:01:47 2025 ———
    7192 
    7193 opened ChimeraX session 
    7194 
    7195 > open 8vWi
    7196 
    7197 8vwi title: 
    7198 The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised
    7199 reconstruction) [more info...] 
    7200  
    7201 Chain information for 8vwi #18 
    7202 --- 
    7203 Chain | Description | UniProt 
    7204 A B C D E F V W X Y Z a | Major capsid protein | MCP_NPVAC 1-347 
    7205 G H I b c d | Capsid-associated protein VP80 | VP80_NPVAC 1-691 
    7206 J M Q S e h | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 
    7207 K L R T f g | Protein C42 | C42_NPVAC 1-361 
    7208 N i | Protein AC109 | AC109_NPVAC 1-390 
    7209 O j | Protein AC142 | AC142_NPVAC 1-477 
    7210 P k | 38K (AC98) protein in P143-LEF5 intergenic region | 38K_NPVAC 1-320 
    7211  
    7212 Non-standard residues in 8vwi #18 
    7213 --- 
    7214 ZN — zinc ion 
    7215  
    7216 
    7217 > select #13/G,H,I
    7218 
    7219 5001 atoms, 5096 bonds, 2 pseudobonds, 611 residues, 2 models selected 
    7220 
    7221 > select #18/G,H,I
    7222 
    7223 10481 atoms, 10589 bonds, 1 pseudobond, 628 residues, 2 models selected 
    7224 
    7225 > select ~sel & ##selected
    7226 
    7227 145785 atoms, 147346 bonds, 76 pseudobonds, 8986 residues, 3 models selected 
    7228 
    7229 > delete atoms (#!18 & sel)
    7230 
    7231 > delete bonds (#!18 & sel)
    7232 
    7233 > select #18/G,H,I
    7234 
    7235 10481 atoms, 10589 bonds, 1 pseudobond, 628 residues, 2 models selected 
    7236 
    7237 > hide sel atoms
    7238 
    7239 > show sel cartoons
    7240 
    7241 > ui mousemode right "translate selected models"
    7242 
    7243 > view matrix models #18,1,0,0,-177.91,0,1,0,67.519,0,0,1,91.008
    7244 
    7245 > view matrix models #18,1,0,0,-204.71,0,1,0,191.65,0,0,1,-10.098
    7246 
    7247 > view matrix models #18,1,0,0,31.513,0,1,0,239.83,0,0,1,100.46
    7248 
    7249 > ui tool show "Fit in Map"
    7250 
    7251 > fitmap #18 inMap #3
    7252 
    7253 Fit molecule 8vwi (#18) to map emd_51808.map (#3) using 10481 atoms 
    7254 average map value = 0.006444, steps = 228 
    7255 shifted from previous position = 18.1 
    7256 rotated from previous position = 42.1 degrees 
    7257 atoms outside contour = 6594, contour level = 0.0074163 
    7258  
    7259 Position of 8vwi (#18) relative to emd_51808.map (#3) coordinates: 
    7260 Matrix rotation and translation 
    7261 0.72238697 -0.69121237 -0.01955832 342.84555920 
    7262 0.69141014 0.72244279 0.00533183 82.71455050 
    7263 0.01044434 -0.01737447 0.99979450 103.81022114 
    7264 Axis -0.01641655 -0.02169179 0.99962991 
    7265 Axis point 66.63545589 471.53150882 0.00000000 
    7266 Rotation angle (degrees) 43.75429421 
    7267 Shift along axis 96.34923300 
    7268  
    7269 
    7270 > hide #!8 models
    7271 
    7272 > show #!8 models
    7273 
    7274 > hide #!11 models
    7275 
    7276 > show #!11 models
    7277 
    7278 > hide #!14 models
    7279 
    7280 > show #!14 models
    7281 
    7282 > hide #!13 models
    7283 
    7284 > show #!13 models
    7285 
    7286 > hide #!16 models
    7287 
    7288 > show #!16 models
    7289 
    7290 > hide #!12 models
    7291 
    7292 > show #!12 models
    7293 
    7294 > hide #!12 models
    7295 
    7296 > hide #!9 models
    7297 
    7298 > show #!9 models
    7299 
    7300 > close #12
    7301 
    7302 > hide #!8 models
    7303 
    7304 > show #!8 models
    7305 
    7306 > hide #!8 models
    7307 
    7308 > show #!8 models
    7309 
    7310 > select subtract #18
    7311 
    7312 Nothing selected 
    7313 
    7314 > hide #!18 models
    7315 
    7316 > show #!18 models
    7317 
    7318 > hide #!8 models
    7319 
    7320 > show #!8 models
    7321 
    7322 > hide #!8 models
    7323 
    7324 > graphics silhouettes true
    7325 
    7326 > lighting depthCue false
    7327 
    7328 > lighting soft
    7329 
    7330 > graphics bgColor white
    7331 
    7332 > graphics silhouettes width 2.1
    7333 
    7334 > cartoon style protein modeHelix tube radius 1.9 sides 24
    7335 
    7336 > select clear
    7337 
    7338 > select #18/G
    7339 
    7340 3228 atoms, 3263 bonds, 194 residues, 1 model selected 
    7341 
    7342 > color sel #732433ff
    7343 
    7344 > select clear
    7345 
    7346 > select #18/H
    7347 
    7348 3513 atoms, 3549 bonds, 210 residues, 1 model selected 
    7349 
    7350 > color sel #fb5e85ff
    7351 
    7352 > select #18/I
    7353 
    7354 3740 atoms, 3777 bonds, 1 pseudobond, 224 residues, 2 models selected 
    7355 
    7356 > color (#!18 & sel) #d87a90ff
    7357 
    7358 > select clear
    7359 
    7360 > select #18/H
    7361 
    7362 3513 atoms, 3549 bonds, 210 residues, 1 model selected 
    7363 
    7364 > color sel #fb5d84ff
    7365 
    7366 > select clear
    7367 
    7368 > color #2,7,9-11,13-18 #fb5174ff
    7369 
    7370 > undo
    7371 
    7372 > select #18/H
    7373 
    7374 3513 atoms, 3549 bonds, 210 residues, 1 model selected 
    7375 
    7376 > color sel #fb5377ff
    7377 
    7378 > select clear
    7379 
    7380 > open (H2J
    7381 
    7382 '(H2J' has no suffix 
    7383 
    7384 > open 9H2J
    7385 
    7386 9h2j title: 
    7387 AcMNPV apical cap - C14 anchor complex only [more info...] 
    7388  
    7389 Chain information for 9h2j #12 
    7390 --- 
    7391 Chain | Description | UniProt 
    7392 A B | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 
    7393 C D | Protein C42 | C42_NPVAC 1-361 
    7394 E | Protein AC142 | AC142_NPVAC 1-477 
    7395 F G L M | Major capsid protein | MCP_NPVAC 1-347 
    7396 H I J | Capsid-associated protein VP80 | VP80_NPVAC 1-691 
    7397 K | Protein AC109 | AC109_NPVAC 1-390 
    7398 N P | Protein Ac66 | AC66_NPVAC 1-808 
    7399 O | Tyrosine-protein phosphatase | PTP_NPVAC 1-168 
    7400  
    7401 Non-standard residues in 9h2j #12 
    7402 --- 
    7403 ZN — zinc ion 
    7404  
    7405 9h2j mmCIF Assemblies 
    7406 --- 
    7407 1| author_defined_assembly 
    7408  
    7409 
    7410 > select #12?H-J
    7411 
    7412 Expected an objects specifier or a keyword 
    7413 
    7414 > select #12/H-J
    7415 
    7416 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    7417 
    7418 > select ~sel & ##selected
    7419 
    7420 23413 atoms, 23880 bonds, 44 pseudobonds, 2869 residues, 3 models selected 
    7421 
    7422 > delete atoms (#!12 & sel)
    7423 
    7424 > delete bonds (#!12 & sel)
    7425 
    7426 > show #!9-15,18 cartoons
    7427 
    7428 > hide #!9-15,18 atoms
    7429 
    7430 > fitmap #12 inMap #3
    7431 
    7432 Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms 
    7433 average map value = 0.008124, steps = 88 
    7434 shifted from previous position = 11.8 
    7435 rotated from previous position = 1.54 degrees 
    7436 atoms outside contour = 2070, contour level = 0.0074163 
    7437  
    7438 Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates: 
    7439 Matrix rotation and translation 
    7440 0.99999318 -0.00273077 -0.00248509 2.24305554 
    7441 0.00273330 0.99999575 0.00101599 -1.59564477 
    7442 0.00248230 -0.00102278 0.99999640 -0.60594412 
    7443 Axis -0.26613114 -0.64841793 0.71325199 
    7444 Axis point 583.74973499 820.48092021 0.00000000 
    7445 Rotation angle (degrees) 0.21946567 
    7446 Shift along axis 0.00550691 
    7447  
    7448 
    7449 > hide #!12 models
    7450 
    7451 > show #!12 models
    7452 
    7453 > hide #!18 models
    7454 
    7455 > show #!18 models
    7456 
    7457 > hide #!18 models
    7458 
    7459 > show #!18 models
    7460 
    7461 > hide #!18 models
    7462 
    7463 > select add #12
    7464 
    7465 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    7466 
    7467 > view matrix models
    7468 > #12,0.99964,0.026795,-0.0024543,-102.14,-0.026792,0.99964,0.001089,34.149,0.0024826,-0.0010229,1,-12.381
    7469 
    7470 > fitmap #12 inMap #3
    7471 
    7472 Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms 
    7473 average map value = 0.00805, steps = 168 
    7474 shifted from previous position = 9.61 
    7475 rotated from previous position = 25.7 degrees 
    7476 atoms outside contour = 2122, contour level = 0.0074163 
    7477  
    7478 Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates: 
    7479 Matrix rotation and translation 
    7480 0.90005241 -0.43577435 -0.00252616 182.09251361 
    7481 0.43577488 0.90005562 -0.00036259 -113.29637229 
    7482 0.00243169 -0.00077449 0.99999674 -0.70368562 
    7483 Axis -0.00047260 -0.00568846 0.99998371 
    7484 Axis point 338.04374149 340.32702583 0.00000000 
    7485 Rotation angle (degrees) 25.83504600 
    7486 Shift along axis -0.14524922 
    7487  
    7488 
    7489 > show #!18 models
    7490 
    7491 > select clear
    7492 
    7493 > hide #!12 models
    7494 
    7495 > show #!12 models
    7496 
    7497 > hide #!18 models
    7498 
    7499 > hide #!9 models
    7500 
    7501 > show #!9 models
    7502 
    7503 > hide #!9 models
    7504 
    7505 > show #!9 models
    7506 
    7507 > hide #!9 models
    7508 
    7509 > close #9-11
    7510 
    7511 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    7512 
    7513 > graphics silhouettes true
    7514 
    7515 > lighting depthCue false
    7516 
    7517 > lighting soft
    7518 
    7519 > graphics bgColor white
    7520 
    7521 > graphics silhouettes width 2.1
    7522 
    7523 > cartoon style protein modeHelix tube radius 1.9 sides 24
    7524 
    7525 > select clear
    7526 
    7527 > volume usage
    7528 
    7529 Expected a density maps specifier or a keyword 
    7530 
    7531 > usasge volume
    7532 
    7533 Unknown command: usasge volume 
    7534 
    7535 > volume zone #3 nearAtoms #12/H-J newMap true
    7536 
    7537 Opened emd_51808.map zone as #9, grid size 500,500,500, pixel 1.35, shown at
    7538 step 1, values float32 
    7539 
    7540 > show #!18 models
    7541 
    7542 > hide #!18 models
    7543 
    7544 > close #18
    7545 
    7546 > show #!3 models
    7547 
    7548 > hide #!7 models
    7549 
    7550 > show #!7 models
    7551 
    7552 > hide #!7 models
    7553 
    7554 > show #!7 models
    7555 
    7556 > hide #!3 models
    7557 
    7558 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    7559 
    7560 ——— End of log from Wed Jun 18 01:06:40 2025 ———
    7561 
    7562 opened ChimeraX session 
    7563 
    7564 > hide #!15 models
    7565 
    7566 > hide #!14 models
    7567 
    7568 > hide #!13 models
    7569 
    7570 > show #!13 models
    7571 
    7572 > hide #!16 models
    7573 
    7574 > hide #!9 models
    7575 
    7576 > hide #!7 models
    7577 
    7578 > show #!7 models
    7579 
    7580 > hide #!17 models
    7581 
    7582 > show #!17 models
    7583 
    7584 > close #17
    7585 
    7586 > show #!3 models
    7587 
    7588 > hide #!7 models
    7589 
    7590 > show #!7 models
    7591 
    7592 > hide #!7 models
    7593 
    7594 > hide #!3 models
    7595 
    7596 > select #12/J:534
    7597 
    7598 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7599 
    7600 > select up
    7601 
    7602 82 atoms, 82 bonds, 10 residues, 1 model selected 
    7603 
    7604 > select up
    7605 
    7606 340 atoms, 348 bonds, 41 residues, 1 model selected 
    7607 
    7608 > select up
    7609 
    7610 407 atoms, 414 bonds, 49 residues, 1 model selected 
    7611 
    7612 > select up
    7613 
    7614 1430 atoms, 1460 bonds, 171 residues, 1 model selected 
    7615 
    7616 > select up
    7617 
    7618 4686 atoms, 4782 bonds, 561 residues, 1 model selected 
    7619 
    7620 > select down
    7621 
    7622 1430 atoms, 1460 bonds, 171 residues, 1 model selected 
    7623 
    7624 > select #12/J
    7625 
    7626 1430 atoms, 1460 bonds, 2 pseudobonds, 171 residues, 2 models selected 
    7627 
    7628 > color (#!12 & sel) #491620ff
    7629 
    7630 > color (#!12 & sel) #491621ff
    7631 
    7632 [Repeated 1 time(s)]
    7633 
    7634 > color (#!12 & sel) #4a1721ff
    7635 
    7636 > color (#!12 & sel) #4d1823ff
    7637 
    7638 > color (#!12 & sel) #541a26ff
    7639 
    7640 > color (#!12 & sel) #571b27ff
    7641 
    7642 > color (#!12 & sel) #631e2cff
    7643 
    7644 [Repeated 1 time(s)]
    7645 
    7646 > color (#!12 & sel) #68202fff
    7647 
    7648 [Repeated 1 time(s)]
    7649 
    7650 > color (#!12 & sel) #6a2130ff
    7651 
    7652 > color (#!12 & sel) #631f2dff
    7653 
    7654 > color (#!12 & sel) #5e1d2aff
    7655 
    7656 > color (#!12 & sel) #5c1c2aff
    7657 
    7658 > color (#!12 & sel) #591b28ff
    7659 
    7660 > color (#!12 & sel) #571b27ff
    7661 
    7662 > color (#!12 & sel) #551a26ff
    7663 
    7664 > color (#!12 & sel) #521925ff
    7665 
    7666 > color (#!12 & sel) #5c1c29ff
    7667 
    7668 > color (#!12 & sel) #5d1d2aff
    7669 
    7670 > color (#!12 & sel) #5e1d2aff
    7671 
    7672 [Repeated 1 time(s)]
    7673 
    7674 > color (#!12 & sel) #5e1e2bff
    7675 
    7676 [Repeated 1 time(s)]
    7677 
    7678 > color (#!12 & sel) #5e1e2aff
    7679 
    7680 [Repeated 3 time(s)]
    7681 
    7682 > color (#!12 & sel) #5e1d28ff
    7683 
    7684 > color (#!12 & sel) #5e1d26ff
    7685 
    7686 > color (#!12 & sel) #5e1d25ff
    7687 
    7688 [Repeated 1 time(s)]
    7689 
    7690 > color (#!12 & sel) #5e1c24ff
    7691 
    7692 > color (#!12 & sel) #5e1d23ff
    7693 
    7694 > color (#!12 & sel) #5e1d20ff
    7695 
    7696 > color (#!12 & sel) #5e1d1fff
    7697 
    7698 [Repeated 1 time(s)]
    7699 
    7700 > color (#!12 & sel) #5e1c1eff
    7701 
    7702 > color (#!12 & sel) #5e1b1eff
    7703 
    7704 > color (#!12 & sel) #5e1b1fff
    7705 
    7706 > color (#!12 & sel) #5e1a1fff
    7707 
    7708 > color (#!12 & sel) #5e191fff
    7709 
    7710 > color (#!12 & sel) #5e1820ff
    7711 
    7712 [Repeated 2 time(s)]
    7713 
    7714 > color (#!12 & sel) #5e1720ff
    7715 
    7716 [Repeated 1 time(s)]
    7717 
    7718 > color (#!12 & sel) #5e1620ff
    7719 
    7720 > color (#!12 & sel) #5e1520ff
    7721 
    7722 > color (#!12 & sel) #5e1421ff
    7723 
    7724 > color (#!12 & sel) #5e1420ff
    7725 
    7726 > color (#!12 & sel) #5e1421ff
    7727 
    7728 > color (#!12 & sel) #5e1321ff
    7729 
    7730 [Repeated 2 time(s)]
    7731 
    7732 > color (#!12 & sel) #5e1221ff
    7733 
    7734 [Repeated 3 time(s)]
    7735 
    7736 > color (#!12 & sel) #5e1220ff
    7737 
    7738 > color (#!12 & sel) #5e1328ff
    7739 
    7740 > color (#!12 & sel) #5e1429ff
    7741 
    7742 > color (#!12 & sel) #5e142aff
    7743 
    7744 > color (#!12 & sel) #5e142bff
    7745 
    7746 [Repeated 1 time(s)]
    7747 
    7748 > color (#!12 & sel) #5e142cff
    7749 
    7750 [Repeated 1 time(s)]
    7751 
    7752 > color (#!12 & sel) #5e142eff
    7753 
    7754 > color (#!12 & sel) #5e142fff
    7755 
    7756 > color (#!12 & sel) #5e1530ff
    7757 
    7758 [Repeated 1 time(s)]
    7759 
    7760 > select clear
    7761 
    7762 > select #12/i
    7763 
    7764 1462 atoms, 1493 bonds, 176 residues, 1 model selected 
    7765 
    7766 > color sel #fb5377ff
    7767 
    7768 > color sel #fb547aff
    7769 
    7770 > color sel #fa5379ff
    7771 
    7772 > color sel #f85379ff
    7773 
    7774 > color sel #f75378ff
    7775 
    7776 > color sel #f45176ff
    7777 
    7778 > color sel #f25176ff
    7779 
    7780 > color sel #ef5074ff
    7781 
    7782 > color sel #e94e71ff
    7783 
    7784 > color sel #e34c6eff
    7785 
    7786 > color sel #e14b6dff
    7787 
    7788 > color sel #df4b6cff
    7789 
    7790 > color sel #da496aff
    7791 
    7792 > color sel #d64768ff
    7793 
    7794 > color sel #d34666ff
    7795 
    7796 > color sel #d24666ff
    7797 
    7798 > color sel #d84869ff
    7799 
    7800 > color sel #da496aff
    7801 
    7802 [Repeated 1 time(s)]
    7803 
    7804 > select #12/H
    7805 
    7806 1794 atoms, 1829 bonds, 2 pseudobonds, 214 residues, 2 models selected 
    7807 
    7808 > color (#!12 & sel) #fca5c2ff
    7809 
    7810 > color (#!12 & sel) #fca5c4ff
    7811 
    7812 > color (#!12 & sel) #fba4c3ff
    7813 
    7814 > color (#!12 & sel) #f9a2c1ff
    7815 
    7816 > color (#!12 & sel) #f7a1c0ff
    7817 
    7818 > color (#!12 & sel) #f39ebdff
    7819 
    7820 > color (#!12 & sel) #f29ebcff
    7821 
    7822 > color (#!12 & sel) #ef9cb9ff
    7823 
    7824 > color (#!12 & sel) #ed9bb8ff
    7825 
    7826 > select clear
    7827 
    7828 > close #13-15
    7829 
    7830 > show #!16 models
    7831 
    7832 > close #16
    7833 
    7834 > show #!9 models
    7835 
    7836 > hide #!9 models
    7837 
    7838 > close #9
    7839 
    7840 > show #!8 models
    7841 
    7842 > hide #!8 models
    7843 
    7844 > show #!8 models
    7845 
    7846 > hide #!8 models
    7847 
    7848 > show #!8 models
    7849 
    7850 > hide #!8 models
    7851 
    7852 > show #!8 models
    7853 
    7854 > hide #!8 models
    7855 
    7856 > show #!8 models
    7857 
    7858 > hide #!8 models
    7859 
    7860 > show #!8 models
    7861 
    7862 > show #!3 models
    7863 
    7864 > close #8
    7865 
    7866 > check symmetry #3
    7867 
    7868 Unknown command: check symmetry #3 
    7869 
    7870 > measure symmetry #3
    7871 
    7872 Symmetry emd_51808.map: C2, center 250 250 258 
    7873 
    7874 > show #!7 models
    7875 
    7876 > hide #!7 models
    7877 
    7878 > hide #!2 models
    7879 
    7880 > show #!2 models
    7881 
    7882 > show #!7 models
    7883 
    7884 > combine #12/H-J
    7885 
    7886 > select add #12
    7887 
    7888 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    7889 
    7890 > ui mousemode right "translate selected models"
    7891 
    7892 > view matrix models
    7893 > #12,0.91253,-0.40901,-0.0025361,79.681,0.40901,0.91253,-0.00028776,-103.75,0.0024319,-0.0007747,1,-7.6978
    7894 
    7895 > combine #12/H-J
    7896 
    7897 > select add #8
    7898 
    7899 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected 
    7900 
    7901 > select subtract #12
    7902 
    7903 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    7904 
    7905 > select add #12
    7906 
    7907 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected 
    7908 
    7909 > select add #9
    7910 
    7911 14058 atoms, 14346 bonds, 12 pseudobonds, 1683 residues, 8 models selected 
    7912 
    7913 > view matrix models
    7914 > #12,0.91253,-0.40901,-0.0025361,58.802,0.40901,0.91253,-0.00028776,-111.99,0.0024319,-0.0007747,1,-7.8898,#8,0.91253,-0.40901,-0.0025361,147.97,0.40901,0.91253,-0.00028776,-116.76,0.0024319,-0.0007747,1,-10.964,#9,0.91253,-0.40901,-0.0025361,58.802,0.40901,0.91253,-0.00028776,-111.99,0.0024319,-0.0007747,1,-7.8898
    7915 
    7916 > select subtract #12
    7917 
    7918 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected 
    7919 
    7920 > select subtract #9
    7921 
    7922 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    7923 
    7924 > select subtract #8
    7925 
    7926 Nothing selected 
    7927 
    7928 > view front
    7929 
    7930 > select add #8
    7931 
    7932 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    7933 
    7934 > view matrix models
    7935 > #8,0.91253,-0.40901,-0.0025361,263.05,0.40901,0.91253,-0.00028776,-134.6,0.0024319,-0.0007747,1,-7.0615
    7936 
    7937 > select add #12
    7938 
    7939 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected 
    7940 
    7941 > select subtract #8
    7942 
    7943 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    7944 
    7945 > view matrix models
    7946 > #12,0.91253,-0.40901,-0.0025361,169.62,0.40901,0.91253,-0.00028776,-129.28,0.0024319,-0.0007747,1,-10.558
    7947 
    7948 > ui tool show "Fit in Map"
    7949 
    7950 > fitmap #12 inMap #3
    7951 
    7952 Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms 
    7953 average map value = 0.00805, steps = 220 
    7954 shifted from previous position = 20.8 
    7955 rotated from previous position = 0.0134 degrees 
    7956 atoms outside contour = 2118, contour level = 0.0074163 
    7957  
    7958 Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates: 
    7959 Matrix rotation and translation 
    7960 0.89997855 -0.43592761 -0.00239316 182.16175413 
    7961 0.43592784 0.89998151 -0.00045246 -113.28031022 
    7962 0.00235104 -0.00063604 0.99999703 -0.75164500 
    7963 Axis -0.00021057 -0.00544141 0.99998517 
    7964 Axis point 337.94735710 340.33112542 0.00000000 
    7965 Rotation angle (degrees) 25.84475250 
    7966 Shift along axis -0.17358585 
    7967  
    7968 
    7969 > fitmap #9 inMap #3
    7970 
    7971 Fit molecule copy of 9h2j (#9) to map emd_51808.map (#3) using 4686 atoms 
    7972 average map value = 0.008067, steps = 192 
    7973 shifted from previous position = 18.8 
    7974 rotated from previous position = 25.7 degrees 
    7975 atoms outside contour = 2099, contour level = 0.0074163 
    7976  
    7977 Position of copy of 9h2j (#9) relative to emd_51808.map (#3) coordinates: 
    7978 Matrix rotation and translation 
    7979 0.62158229 -0.78334695 -0.00173858 393.14200315 
    7980 0.78334624 0.62158442 -0.00121467 -136.11104005 
    7981 0.00203218 -0.00060689 0.99999775 -0.63815363 
    7982 Axis 0.00038793 -0.00240681 0.99999703 
    7983 Axis point 337.45120495 338.85949584 0.00000000 
    7984 Rotation angle (degrees) 51.56823043 
    7985 Shift along axis -0.15804494 
    7986  
    7987 
    7988 > fitmap #8 inMap #3
    7989 
    7990 Fit molecule copy of 9h2j (#8) to map emd_51808.map (#3) using 4686 atoms 
    7991 average map value = 0.008124, steps = 172 
    7992 shifted from previous position = 9.7 
    7993 rotated from previous position = 25.7 degrees 
    7994 atoms outside contour = 2069, contour level = 0.0074163 
    7995  
    7996 Position of copy of 9h2j (#8) relative to emd_51808.map (#3) coordinates: 
    7997 Matrix rotation and translation 
    7998 0.99999359 -0.00272428 -0.00232336 2.18361006 
    7999 0.00272673 0.99999573 0.00104894 -1.60363375 
    8000 0.00232049 -0.00105526 0.99999675 -0.51987891 
    8001 Axis -0.28192500 -0.62219354 0.73033793 
    8002 Axis point 588.80595766 800.40533547 0.00000000 
    8003 Rotation angle (degrees) 0.21381932 
    8004 Shift along axis 0.00246900 
    8005  
    8006 
    8007 > select clear
    8008 
    8009 > combine #12/H-J
    8010 
    8011 > select add #8
    8012 
    8013 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8014 
    8015 > select add #9
    8016 
    8017 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected 
    8018 
    8019 > select add #10
    8020 
    8021 14058 atoms, 14346 bonds, 12 pseudobonds, 1683 residues, 9 models selected 
    8022 
    8023 > select subtract #9
    8024 
    8025 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected 
    8026 
    8027 > select subtract #8
    8028 
    8029 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8030 
    8031 > select add #12
    8032 
    8033 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected 
    8034 
    8035 > select subtract #12
    8036 
    8037 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8038 
    8039 > view matrix models
    8040 > #10,0.91246,-0.40917,-0.0024058,-5.2451,0.40917,0.91246,-0.00038152,-117.68,0.0023513,-0.00063625,1,-1.7477
    8041 
    8042 > view matrix models
    8043 > #10,0.91246,-0.40917,-0.0024058,6.0685,0.40917,0.91246,-0.00038152,-167.41,0.0023513,-0.00063625,1,17.238
    8044 
    8045 > fitmap #10 inMap #3
    8046 
    8047 Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms 
    8048 average map value = 0.005529, steps = 148 
    8049 shifted from previous position = 22.2 
    8050 rotated from previous position = 6.12 degrees 
    8051 atoms outside contour = 3059, contour level = 0.0074163 
    8052  
    8053 Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates: 
    8054 Matrix rotation and translation 
    8055 0.90204797 -0.42538232 0.07320748 -2.12972818 
    8056 0.42047121 0.90431073 0.07366184 -216.34367525 
    8057 -0.09753675 -0.03566488 0.99459268 84.18985729 
    8058 Axis -0.12568996 0.19630000 0.97245480 
    8059 Axis point 507.95649835 -110.25127704 0.00000000 
    8060 Rotation angle (degrees) 25.77933457 
    8061 Shift along axis 39.67025376 
    8062  
    8063 
    8064 > fitmap #10 inMap #3
    8065 
    8066 Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms 
    8067 average map value = 0.005529, steps = 60 
    8068 shifted from previous position = 0.019 
    8069 rotated from previous position = 0.00947 degrees 
    8070 atoms outside contour = 3062, contour level = 0.0074163 
    8071  
    8072 Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates: 
    8073 Matrix rotation and translation 
    8074 0.90205379 -0.42539478 0.07306326 -2.06098965 
    8075 0.42049649 0.90430530 0.07358412 -216.31682850 
    8076 -0.09737379 -0.03565399 0.99460904 84.10348636 
    8077 Axis -0.12559310 0.19595466 0.97253696 
    8078 Axis point 507.86667095 -110.06962014 0.00000000 
    8079 Rotation angle (degrees) 25.77823154 
    8080 Shift along axis 39.66430515 
    8081  
    8082 
    8083 > view matrix models
    8084 > #10,0.91408,-0.39851,0.075204,-36.692,0.39368,0.91647,0.071395,-201.29,-0.097374,-0.035654,0.99461,51.872
    8085 
    8086 > fitmap #10 inMap #3
    8087 
    8088 Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms 
    8089 average map value = 0.008103, steps = 488 
    8090 shifted from previous position = 15.9 
    8091 rotated from previous position = 52.5 degrees 
    8092 atoms outside contour = 2069, contour level = 0.0074163 
    8093  
    8094 Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates: 
    8095 Matrix rotation and translation 
    8096 0.22005060 -0.97548761 -0.00128377 593.25703314 
    8097 0.97548641 0.22005264 -0.00175945 -65.05565033 
    8098 0.00199882 -0.00086514 0.99999763 -0.48706362 
    8099 Axis 0.00045839 -0.00168254 0.99999848 
    8100 Axis point 337.31158469 338.46776553 0.00000000 
    8101 Rotation angle (degrees) 77.28800469 
    8102 Shift along axis -0.10565891 
    8103  
    8104 
    8105 > fitmap #10 inMap #3
    8106 
    8107 Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms 
    8108 average map value = 0.008103, steps = 76 
    8109 shifted from previous position = 0.00242 
    8110 rotated from previous position = 0.00552 degrees 
    8111 atoms outside contour = 2069, contour level = 0.0074163 
    8112  
    8113 Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates: 
    8114 Matrix rotation and translation 
    8115 0.21999869 -0.97549939 -0.00123397 593.26836800 
    8116 0.97549826 0.22000059 -0.00169656 -65.05737940 
    8117 0.00192647 -0.00083049 0.99999780 -0.47258372 
    8118 Axis 0.00044391 -0.00161991 0.99999859 
    8119 Axis point 337.31609761 338.45374235 0.00000000 
    8120 Rotation angle (degrees) 77.29105268 
    8121 Shift along axis -0.10383708 
    8122  
    8123 
    8124 > select subtract #10
    8125 
    8126 Nothing selected 
    8127 
    8128 > combine #12/H-J
    8129 
    8130 > select add #11
    8131 
    8132 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8133 
    8134 > view matrix models
    8135 > #11,0.91246,-0.40917,-0.0024058,325.71,0.40917,0.91246,-0.00038152,-194.43,0.0023513,-0.00063625,1,-1.127
    8136 
    8137 > fitmap #11 inMap #3
    8138 
    8139 Fit molecule copy of 9h2j (#11) to map emd_51808.map (#3) using 4686 atoms 
    8140 average map value = 0.008113, steps = 328 
    8141 shifted from previous position = 16.3 
    8142 rotated from previous position = 51.4 degrees 
    8143 atoms outside contour = 2068, contour level = 0.0074163 
    8144  
    8145 Position of copy of 9h2j (#11) relative to emd_51808.map (#3) coordinates: 
    8146 Matrix rotation and translation 
    8147 0.90217111 0.43137547 -0.00158165 -111.75969148 
    8148 -0.43137241 0.90217185 0.00194823 177.46726907 
    8149 0.00226734 -0.00107535 0.99999685 -0.48439830 
    8150 Axis -0.00350454 -0.00446125 -0.99998391 
    8151 Axis point 335.39824842 335.13967814 0.00000000 
    8152 Rotation angle (degrees) 25.55522633 
    8153 Shift along axis 0.08433080 
    8154  
    8155 
    8156 > view front
    8157 
    8158 > combine #12/H-J
    8159 
    8160 > select add #13
    8161 
    8162 9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected 
    8163 
    8164 > select subtract #11
    8165 
    8166 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8167 
    8168 > view matrix models
    8169 > #13,0.91246,-0.40917,-0.0024058,342.27,0.40917,0.91246,-0.00038152,-286.57,0.0023513,-0.00063625,1,5.0769
    8170 
    8171 > fitmap #13 inMap #3
    8172 
    8173 Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms 
    8174 average map value = 0.00562, steps = 312 
    8175 shifted from previous position = 21.6 
    8176 rotated from previous position = 49.8 degrees 
    8177 atoms outside contour = 3231, contour level = 0.0074163 
    8178  
    8179 Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates: 
    8180 Matrix rotation and translation 
    8181 0.91945451 0.38746306 0.06690132 -99.31052235 
    8182 -0.39318178 0.90748090 0.14794085 20.81499994 
    8183 -0.00339006 -0.16232926 0.98673082 86.01920655 
    8184 Axis -0.36806356 0.08338443 -0.92605413 
    8185 Axis point -7.47986169 294.05363565 0.00000000 
    8186 Rotation angle (degrees) 24.92868391 
    8187 Shift along axis -41.37020973 
    8188  
    8189 
    8190 > fitmap #13 inMap #3
    8191 
    8192 Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms 
    8193 average map value = 0.00562, steps = 44 
    8194 shifted from previous position = 0.00607 
    8195 rotated from previous position = 0.00809 degrees 
    8196 atoms outside contour = 3232, contour level = 0.0074163 
    8197  
    8198 Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates: 
    8199 Matrix rotation and translation 
    8200 0.91949117 0.38736217 0.06698166 -99.30442707 
    8201 -0.39309512 0.90752455 0.14790342 20.76658332 
    8202 -0.00349531 -0.16232605 0.98673098 86.06984775 
    8203 Axis -0.36809096 0.08362176 -0.92602184 
    8204 Axis point -7.55882537 294.14233104 0.00000000 
    8205 Rotation angle (degrees) 24.92321429 
    8206 Shift along axis -41.41295932 
    8207  
    8208 
    8209 > view matrix models
    8210 > #13,0.90748,0.41399,0.071319,-92.991,-0.42007,0.89569,0.14586,25.823,-0.003495,-0.16233,0.98673,84.261
    8211 
    8212 > fitmap #13 inMap #3
    8213 
    8214 Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms 
    8215 average map value = 0.008043, steps = 188 
    8216 shifted from previous position = 10.3 
    8217 rotated from previous position = 29.6 degrees 
    8218 atoms outside contour = 2110, contour level = 0.0074163 
    8219  
    8220 Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates: 
    8221 Matrix rotation and translation 
    8222 0.62540387 0.78030080 -0.00080651 -136.64337522 
    8223 -0.78029751 0.62540375 0.00243810 388.44994392 
    8224 0.00240685 -0.00089548 0.99999670 -0.64198151 
    8225 Axis -0.00213608 -0.00205905 -0.99999560 
    8226 Axis point 336.25961586 336.54282700 0.00000000 
    8227 Rotation angle (degrees) 51.28828857 
    8228 Shift along axis 0.13402367 
    8229  
    8230 
    8231 > fitmap #13 inMap #3
    8232 
    8233 Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms 
    8234 average map value = 0.008043, steps = 44 
    8235 shifted from previous position = 0.0249 
    8236 rotated from previous position = 0.00832 degrees 
    8237 atoms outside contour = 2103, contour level = 0.0074163 
    8238  
    8239 Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates: 
    8240 Matrix rotation and translation 
    8241 0.62548870 0.78023290 -0.00071051 -136.65886359 
    8242 -0.78022971 0.62548836 0.00243151 388.38578651 
    8243 0.00234156 -0.00096653 0.99999679 -0.58976226 
    8244 Axis -0.00217757 -0.00195586 -0.99999572 
    8245 Axis point 336.24125162 336.54660427 0.00000000 
    8246 Rotation angle (degrees) 51.28206464 
    8247 Shift along axis 0.12771450 
    8248  
    8249 
    8250 > fitmap #13 inMap #3
    8251 
    8252 Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms 
    8253 average map value = 0.008043, steps = 48 
    8254 shifted from previous position = 0.0296 
    8255 rotated from previous position = 0.0116 degrees 
    8256 atoms outside contour = 2112, contour level = 0.0074163 
    8257  
    8258 Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates: 
    8259 Matrix rotation and translation 
    8260 0.62550544 0.78021964 -0.00051153 -136.74508465 
    8261 -0.78021671 0.62550467 0.00240450 388.36971399 
    8262 0.00219600 -0.00110492 0.99999698 -0.43341938 
    8263 Axis -0.00224899 -0.00173511 -0.99999597 
    8264 Axis point 336.19205086 336.63216766 0.00000000 
    8265 Rotation angle (degrees) 51.28084399 
    8266 Shift along axis 0.06709267 
    8267  
    8268 
    8269 > combine #12/H-J
    8270 
    8271 > select subtract #13
    8272 
    8273 Nothing selected 
    8274 
    8275 > select add #14
    8276 
    8277 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected 
    8278 
    8279 > view matrix models
    8280 > #14,0.91246,-0.40917,-0.0024058,-63.704,0.40917,0.91246,-0.00038152,-199.82,0.0023513,-0.00063625,1,6.8614
    8281 
    8282 > view matrix models
    8283 > #14,0.91246,-0.40917,-0.0024058,-47.684,0.40917,0.91246,-0.00038152,-236.16,0.0023513,-0.00063625,1,19.227
    8284 
    8285 > fitmap #14 inMap #3
    8286 
    8287 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8288 average map value = 0.005454, steps = 156 
    8289 shifted from previous position = 22.7 
    8290 rotated from previous position = 20.5 degrees 
    8291 atoms outside contour = 3124, contour level = 0.0074163 
    8292  
    8293 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8294 Matrix rotation and translation 
    8295 0.96735530 -0.25166263 0.02982690 -150.11807775 
    8296 0.23252009 0.92820125 0.29047693 -282.33790136 
    8297 -0.10078756 -0.27405905 0.95641702 222.35437906 
    8298 Axis -0.74761901 0.17297366 0.64120662 
    8299 Axis point 0.00000000 149.48567957 1131.58050632 
    8300 Rotation angle (degrees) 22.18237314 
    8301 Shift along axis 205.96920963 
    8302  
    8303 
    8304 > fitmap #14 inMap #3
    8305 
    8306 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8307 average map value = 0.005454, steps = 64 
    8308 shifted from previous position = 0.0238 
    8309 rotated from previous position = 0.00196 degrees 
    8310 atoms outside contour = 3125, contour level = 0.0074163 
    8311  
    8312 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8313 Matrix rotation and translation 
    8314 0.96734788 -0.25169019 0.02983494 -150.09959510 
    8315 0.23254254 0.92819033 0.29049386 -282.33058598 
    8316 -0.10080695 -0.27407073 0.95641162 222.38668885 
    8317 Axis -0.74759928 0.17299665 0.64122343 
    8318 Axis point 0.00000000 149.56426002 1131.53218767 
    8319 Rotation angle (degrees) 22.18417383 
    8320 Shift along axis 205.97165777 
    8321  
    8322 
    8323 > view matrix models
    8324 > #14,0.97379,-0.22418,0.038398,-189.36,0.20388,0.93522,0.28949,-268.17,-0.10081,-0.27407,0.95641,209.17
    8325 
    8326 > fitmap #14 inMap #3
    8327 
    8328 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8329 average map value = 0.005454, steps = 156 
    8330 shifted from previous position = 21.4 
    8331 rotated from previous position = 0.00948 degrees 
    8332 atoms outside contour = 3131, contour level = 0.0074163 
    8333  
    8334 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8335 Matrix rotation and translation 
    8336 0.96736636 -0.25160849 0.02992493 -150.16985353 
    8337 0.23245091 0.92824741 0.29038477 -282.28830679 
    8338 -0.10084101 -0.27395238 0.95644194 222.32675316 
    8339 Axis -0.74755518 0.17322049 0.64121441 
    8340 Axis point 0.00000000 149.59849898 1131.91943807 
    8341 Rotation angle (degrees) 22.17613946 
    8342 Shift along axis 205.92125140 
    8343  
    8344 
    8345 > view matrix models
    8346 > #14,0.97381,-0.22409,0.038485,-187.42,0.20379,0.93527,0.28937,-281.11,-0.10084,-0.27395,0.95644,193.55
    8347 
    8348 > fitmap #14 inMap #3
    8349 
    8350 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8351 average map value = 0.005057, steps = 148 
    8352 shifted from previous position = 16.7 
    8353 rotated from previous position = 21.6 degrees 
    8354 atoms outside contour = 3453, contour level = 0.0074163 
    8355  
    8356 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8357 Matrix rotation and translation 
    8358 0.84743544 -0.43092698 0.31008889 -111.61706948 
    8359 0.28405814 0.86148443 0.42089850 -314.68029233 
    8360 -0.44851327 -0.26860103 0.85246075 383.67953894 
    8361 Axis -0.55167191 0.60696126 0.57206305 
    8362 Axis point 580.86386831 0.00000000 485.50385093 
    8363 Rotation angle (degrees) 38.67617687 
    8364 Shift along axis 90.06614474 
    8365  
    8366 
    8367 > fitmap #14 inMap #3
    8368 
    8369 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8370 average map value = 0.005057, steps = 48 
    8371 shifted from previous position = 0.00732 
    8372 rotated from previous position = 0.0298 degrees 
    8373 atoms outside contour = 3451, contour level = 0.0074163 
    8374  
    8375 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8376 Matrix rotation and translation 
    8377 0.84745061 -0.43063705 0.31044999 -111.90017932 
    8378 0.28360755 0.86159562 0.42097476 -314.56494215 
    8379 -0.44876968 -0.26870935 0.85229165 383.91108390 
    8380 Axis -0.55179602 0.60742938 0.57144615 
    8381 Axis point 580.89812132 -0.00000000 485.82403723 
    8382 Rotation angle (degrees) 38.67813643 
    8383 Shift along axis 90.05459612 
    8384  
    8385 
    8386 > fitmap #14 inMap #3
    8387 
    8388 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8389 average map value = 0.005057, steps = 48 
    8390 shifted from previous position = 0.00826 
    8391 rotated from previous position = 0.0316 degrees 
    8392 atoms outside contour = 3454, contour level = 0.0074163 
    8393  
    8394 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8395 Matrix rotation and translation 
    8396 0.84749889 -0.43088450 0.30997448 -111.63021772 
    8397 0.28399936 0.86145527 0.42099783 -314.67270743 
    8398 -0.44843059 -0.26876264 0.85245331 383.72612953 
    8399 Axis -0.55189550 0.60681985 0.57199739 
    8400 Axis point 580.99005721 0.00000000 485.45630776 
    8401 Rotation angle (degrees) 38.67494585 
    8402 Shift along axis 90.14891535 
    8403  
    8404 
    8405 > view matrix models
    8406 > #14,0.85551,-0.40526,0.32227,-141.21,0.25885,0.8738,0.41166,-302.29,-0.44843,-0.26876,0.85245,371.94
    8407 
    8408 > ui mousemode right "rotate selected models"
    8409 
    8410 > view matrix models
    8411 > #14,0.89716,-0.37034,0.24072,-148.69,0.22136,0.84859,0.48052,-297.16,-0.38223,-0.37782,0.8433,402.24
    8412 
    8413 > view matrix models
    8414 > #14,0.50401,-0.85752,-0.10311,397.1,0.69275,0.33006,0.64122,-294.28,-0.51582,-0.39461,0.7604,499.03
    8415 
    8416 > view matrix models
    8417 > #14,0.26685,-0.87396,0.40618,329.76,0.89852,0.37803,0.22307,-261.63,-0.34851,0.30544,0.88614,20.118
    8418 
    8419 > fitmap #14 inMap #3
    8420 
    8421 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8422 average map value = 0.008053, steps = 184 
    8423 shifted from previous position = 9.18 
    8424 rotated from previous position = 41.6 degrees 
    8425 atoms outside contour = 2100, contour level = 0.0074163 
    8426  
    8427 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8428 Matrix rotation and translation 
    8429 -0.22508318 -0.97433950 -0.00031500 742.60891926 
    8430 0.97433710 -0.22508188 -0.00231503 85.91975961 
    8431 0.00218472 -0.00082799 0.99999727 -0.58981658 
    8432 Axis 0.00076310 -0.00128278 0.99999889 
    8433 Axis point 337.13766431 338.26745131 0.00000000 
    8434 Rotation angle (degrees) 103.00781132 
    8435 Shift along axis -0.13334495 
    8436  
    8437 
    8438 > fitmap #14 inMap #3
    8439 
    8440 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8441 average map value = 0.008053, steps = 48 
    8442 shifted from previous position = 0.00934 
    8443 rotated from previous position = 0.00919 degrees 
    8444 atoms outside contour = 2104, contour level = 0.0074163 
    8445  
    8446 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8447 Matrix rotation and translation 
    8448 -0.22501832 -0.97435449 -0.00029112 742.57206285 
    8449 0.97435175 -0.22501695 -0.00245903 85.92560319 
    8450 0.00233046 -0.00083698 0.99999693 -0.65461631 
    8451 Axis 0.00083237 -0.00134529 0.99999875 
    8452 Axis point 337.11463885 338.27583713 0.00000000 
    8453 Rotation angle (degrees) 103.00400544 
    8454 Shift along axis -0.15211300 
    8455  
    8456 
    8457 > fitmap #14 inMap #3
    8458 
    8459 Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms 
    8460 average map value = 0.008053, steps = 76 
    8461 shifted from previous position = 0.00603 
    8462 rotated from previous position = 0.00676 degrees 
    8463 atoms outside contour = 2100, contour level = 0.0074163 
    8464  
    8465 Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates: 
    8466 Matrix rotation and translation 
    8467 -0.22503991 -0.97434947 -0.00038064 742.61410000 
    8468 0.97434698 -0.22503840 -0.00238541 85.91234090 
    8469 0.00223856 -0.00090769 0.99999708 -0.57415084 
    8470 Axis 0.00075831 -0.00134408 0.99999881 
    8471 Axis point 337.14163687 338.27927836 0.00000000 
    8472 Rotation angle (degrees) 103.00526624 
    8473 Shift along axis -0.12649191 
    8474  
    8475 
    8476 > select clear
    8477 
    8478 > view front
    8479 
    8480 > name veiew front
    8481 
    8482 "front": invalid atom specifier 
    8483 
    8484 > view name front
    8485 
    8486 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    8487 
    8488 > volume zone #3 nearAtoms #8-14/H-J newMap true
    8489 
    8490 Opened emd_51808.map zone as #15, grid size 500,500,500, pixel 1.35, shown at
    8491 step 1, values float32 
    8492 
    8493 > hide #15.1 models
    8494 
    8495 > show #15.1 models
    8496 
    8497 > hide #15.1 models
    8498 
    8499 > show #15.1 models
    8500 
    8501 > hide #15.1 models
    8502 
    8503 > hide #!8-14 atoms
    8504 
    8505 [Repeated 1 time(s)]
    8506 
    8507 > hide #!8-14 cartoons
    8508 
    8509 > show #!8-14 cartoons
    8510 
    8511 [Repeated 1 time(s)]
    8512 
    8513 > hide pbonds
    8514 
    8515 > show #15.1 models
    8516 
    8517 > volume zone #3 nearAtoms #8-14/H-J invertMap truenewMap true
    8518 
    8519 Expected a keyword 
    8520 
    8521 > volume zone #3 nearAtoms #8-14/H-J invertMap true newMap true
    8522 
    8523 Expected a keyword 
    8524 
    8525 > volume zone #3 nearAtoms #8-14/H-J invert true newMap true
    8526 
    8527 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    8528 step 1, values float32 
    8529 
    8530 > volume #16 level 0.006624
    8531 
    8532 > volume #15 level 0.00726
    8533 
    8534 > volume #15 level 0.007312
    8535 
    8536 > color #16 #d2d2d3ff models
    8537 
    8538 > color #16 #f1f2f4ff models
    8539 
    8540 > hide #15.1 models
    8541 
    8542 > show #15.1 models
    8543 
    8544 > hide #!15 models
    8545 
    8546 > show #!15 models
    8547 
    8548 > hide #!15 models
    8549 
    8550 > show #!15 models
    8551 
    8552 > hide #!7 models
    8553 
    8554 > show #!7 models
    8555 
    8556 > color #15 #ff91aaff models
    8557 
    8558 > color #15 #ff91aa41 models
    8559 
    8560 > color #15 #ff91aa54 models
    8561 
    8562 > color #15 #ff91aa68 models
    8563 
    8564 > color #15 #ff91aa66 models
    8565 
    8566 > color #2 #f1f2f4ff models
    8567 
    8568 > color #3 #f1f2f4ff models
    8569 
    8570 > select clear
    8571 
    8572 > color #7 #f1f2f4ff models
    8573 
    8574 > volume zone #3 nearAtoms #8-14/H-J range 4 newMap true
    8575 
    8576 Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
    8577 step 1, values float32 
    8578 
    8579 > hide #!16 models
    8580 
    8581 > hide #!15 models
    8582 
    8583 > show #!15 models
    8584 
    8585 > hide #!15 models
    8586 
    8587 > show #!15 models
    8588 
    8589 > hide #!17 models
    8590 
    8591 > show #!17 models
    8592 
    8593 > hide #!17 models
    8594 
    8595 > show #!17 models
    8596 
    8597 > hide #!17 models
    8598 
    8599 > show #!17 models
    8600 
    8601 > show #!16 models
    8602 
    8603 > color #16 #f1f2f48e models
    8604 
    8605 > volume zone #3 nearAtoms #8-14/H-J range 4 invert true newMap true
    8606 
    8607 Opened emd_51808.map zone as #18, grid size 500,500,500, pixel 1.35, shown at
    8608 step 1, values float32 
    8609 
    8610 > close #15-16
    8611 
    8612 > volume #17 level 0.006994
    8613 
    8614 > volume #18 level 0.006192
    8615 
    8616 > ui tool show "Hide Dust"
    8617 
    8618 > surface dust #2 size 1.35
    8619 
    8620 > surface dust #18 size 15.44
    8621 
    8622 [Repeated 1 time(s)]
    8623 
    8624 > surface dust #18 size 14.68
    8625 
    8626 > surface dust #18 size 19.21
    8627 
    8628 > hide #!17 models
    8629 
    8630 > show #!17 models
    8631 
    8632 > hide #!17 models
    8633 
    8634 > show #!17 models
    8635 
    8636 > color #17 #b2ffff3b models
    8637 
    8638 > hide #!17 models
    8639 
    8640 > show #!17 models
    8641 
    8642 > volume zone #3 nearAtoms #8-14/H-J range 5 invert true newMap true
    8643 
    8644 Opened emd_51808.map zone as #15, grid size 500,500,500, pixel 1.35, shown at
    8645 step 1, values float32 
    8646 
    8647 > hide #!18 models
    8648 
    8649 > show #!18 models
    8650 
    8651 > hide #!18 models
    8652 
    8653 > volume #15 level 0.006264
    8654 
    8655 > surface dust #15 size 8.1
    8656 
    8657 > surface dust #15 size 7.75
    8658 
    8659 > surface dust #15 size 24.31
    8660 
    8661 > close #18
    8662 
    8663 > hide #!15 models
    8664 
    8665 > show #!15 models
    8666 
    8667 > color #15 #f1f2f4ff models
    8668 
    8669 > color #17 #ff91aaff models
    8670 
    8671 > color #17 #ff91aa49 models
    8672 
    8673 > color #17 #ff91aa2b models
    8674 
    8675 > color #17 #ff91aa3d models
    8676 
    8677 > color #17 #ff91aa4d models
    8678 
    8679 > color #17 #ff91aa60 models
    8680 
    8681 > color #17 #ff91aa65 models
    8682 
    8683 > view front
    8684 
    8685 > combine #8-11,13,14
    8686 
    8687 Remapping chain ID 'H' in copy of 9h2j #9 to 'K' 
    8688 Remapping chain ID 'I' in copy of 9h2j #9 to 'L' 
    8689 Remapping chain ID 'J' in copy of 9h2j #9 to 'M' 
    8690 Remapping chain ID 'H' in copy of 9h2j #10 to 'N' 
    8691 Remapping chain ID 'I' in copy of 9h2j #10 to 'O' 
    8692 Remapping chain ID 'J' in copy of 9h2j #10 to 'P' 
    8693 Remapping chain ID 'H' in copy of 9h2j #11 to 'Q' 
    8694 Remapping chain ID 'I' in copy of 9h2j #11 to 'R' 
    8695 Remapping chain ID 'J' in copy of 9h2j #11 to 'S' 
    8696 Remapping chain ID 'H' in copy of 9h2j #13 to 'T' 
    8697 Remapping chain ID 'I' in copy of 9h2j #13 to 'U' 
    8698 Remapping chain ID 'J' in copy of 9h2j #13 to 'V' 
    8699 Remapping chain ID 'H' in copy of 9h2j #14 to 'W' 
    8700 Remapping chain ID 'I' in copy of 9h2j #14 to 'X' 
    8701 Remapping chain ID 'J' in copy of 9h2j #14 to 'Y' 
    8702 
    8703 > select add #16
    8704 
    8705 28116 atoms, 28692 bonds, 24 pseudobonds, 3366 residues, 3 models selected 
    8706 
    8707 > select subtract #16
    8708 
    8709 Nothing selected 
    8710 
    8711 > hide #!16 models
    8712 
    8713 > show #!16 models
    8714 
    8715 > close #8-11
    8716 
    8717 > close #13-14
    8718 
    8719 > hide #!17 models
    8720 
    8721 > show #!17 models
    8722 
    8723 > hide #!16 models
    8724 
    8725 > show #!16 models
    8726 
    8727 > combine #12,16
    8728 
    8729 Remapping chain ID 'H' in combination #16 to 'Z' 
    8730 Remapping chain ID 'I' in combination #16 to 'a' 
    8731 Remapping chain ID 'J' in combination #16 to 'b' 
    8732 
    8733 > select add #8
    8734 
    8735 32802 atoms, 33474 bonds, 28 pseudobonds, 3927 residues, 3 models selected 
    8736 
    8737 > view matrix models
    8738 > #8,-0.92259,0.3699,0.10958,477.16,-0.3563,-0.92589,0.12561,877.74,0.14792,0.076847,0.98601,-90.493
    8739 
    8740 > ui mousemode right "translate selected models"
    8741 
    8742 > view matrix models
    8743 > #8,-0.92259,0.3699,0.10958,500.67,-0.3563,-0.92589,0.12561,718.05,0.14792,0.076847,0.98601,-81.445
    8744 
    8745 > ui tool show "Fit in Map"
    8746 
    8747 > fitmap #8 inMap #3
    8748 
    8749 Fit molecule combination (#8) to map emd_51808.map (#3) using 32802 atoms 
    8750 average map value = 0.008079, steps = 188 
    8751 shifted from previous position = 22.3 
    8752 rotated from previous position = 9.87 degrees 
    8753 atoms outside contour = 14643, contour level = 0.0074163 
    8754  
    8755 Position of combination (#8) relative to emd_51808.map (#3) coordinates: 
    8756 Matrix rotation and translation 
    8757 -0.89994101 0.43600528 0.00236655 492.78893619 
    8758 -0.43600543 -0.89994393 0.00047849 788.29312292 
    8759 0.00233839 -0.00060122 0.99999711 -0.75151604 
    8760 Axis -0.00123818 0.00003230 -0.99999923 
    8761 Axis point 336.84511483 337.60302966 0.00000000 
    8762 Rotation angle (degrees) 154.15069564 
    8763 Shift along axis 0.16681444 
    8764  
    8765 
    8766 > fitmap #8 inMap #3
    8767 
    8768 Fit molecule combination (#8) to map emd_51808.map (#3) using 32802 atoms 
    8769 average map value = 0.008079, steps = 40 
    8770 shifted from previous position = 0.0226 
    8771 rotated from previous position = 0.00386 degrees 
    8772 atoms outside contour = 14631, contour level = 0.0074163 
    8773  
    8774 Position of combination (#8) relative to emd_51808.map (#3) coordinates: 
    8775 Matrix rotation and translation 
    8776 -0.89995651 0.43597358 0.00231330 492.83129699 
    8777 -0.43597365 -0.89995931 0.00049986 788.26495943 
    8778 0.00229980 -0.00055868 0.99999722 -0.77156368 
    8779 Axis -0.00121400 0.00001548 -0.99999926 
    8780 Axis point 336.85574521 337.58866909 0.00000000 
    8781 Rotation angle (degrees) 154.15271718 
    8782 Shift along axis 0.18546542 
    8783  
    8784 
    8785 > select clear
    8786 
    8787 > hide #!16 models
    8788 
    8789 > show #!16 models
    8790 
    8791 > combine #8,16
    8792 
    8793 Remapping chain ID 'H' in combination #16 to 'c' 
    8794 Remapping chain ID 'I' in combination #16 to 'd' 
    8795 Remapping chain ID 'J' in combination #16 to 'e' 
    8796 Remapping chain ID 'K' in combination #16 to 'f' 
    8797 Remapping chain ID 'L' in combination #16 to 'g' 
    8798 Remapping chain ID 'M' in combination #16 to 'h' 
    8799 Remapping chain ID 'N' in combination #16 to 'i' 
    8800 Remapping chain ID 'O' in combination #16 to 'j' 
    8801 Remapping chain ID 'P' in combination #16 to 'k' 
    8802 Remapping chain ID 'Q' in combination #16 to 'l' 
    8803 Remapping chain ID 'R' in combination #16 to 'm' 
    8804 Remapping chain ID 'S' in combination #16 to 'n' 
    8805 Remapping chain ID 'T' in combination #16 to 'o' 
    8806 Remapping chain ID 'U' in combination #16 to 'p' 
    8807 Remapping chain ID 'V' in combination #16 to 'q' 
    8808 Remapping chain ID 'W' in combination #16 to 'r' 
    8809 Remapping chain ID 'X' in combination #16 to 's' 
    8810 Remapping chain ID 'Y' in combination #16 to 't' 
    8811 
    8812 > select add #9
    8813 
    8814 60918 atoms, 62166 bonds, 52 pseudobonds, 7293 residues, 2 models selected 
    8815 
    8816 > select subtract #9
    8817 
    8818 Nothing selected 
    8819 
    8820 > hide #!8 models
    8821 
    8822 > close #8
    8823 
    8824 > close #16
    8825 
    8826 > hide #!17 models
    8827 
    8828 > show #!17 models
    8829 
    8830 > color #17 #ff91aaff models
    8831 
    8832 > hide #!9 models
    8833 
    8834 > show #!9 models
    8835 
    8836 > hide #!17 models
    8837 
    8838 > show #!17 models
    8839 
    8840 > color #17 #ff91aa53 models
    8841 
    8842 > show #!1 models
    8843 
    8844 > hide #!1 models
    8845 
    8846 > show #!1 models
    8847 
    8848 > hide #!1 models
    8849 
    8850 > show #!3 models
    8851 
    8852 > hide #!3 models
    8853 
    8854 > show #!3 models
    8855 
    8856 > hide #!3 models
    8857 
    8858 > show #!4 models
    8859 
    8860 > hide #!4 models
    8861 
    8862 > show #!4 models
    8863 
    8864 > hide #!4 models
    8865 
    8866 > hide #!12 models
    8867 
    8868 > show #!12 models
    8869 
    8870 > hide #!12 models
    8871 
    8872 > show #!12 models
    8873 
    8874 > show #!4 models
    8875 
    8876 > hide #!9 models
    8877 
    8878 > show #!9 models
    8879 
    8880 > hide #!12 models
    8881 
    8882 > close #4
    8883 
    8884 > show #5 models
    8885 
    8886 > hide #5 models
    8887 
    8888 > show #5 models
    8889 
    8890 > hide #5 models
    8891 
    8892 > close #5
    8893 
    8894 > show #!6 models
    8895 
    8896 > hide #!6 models
    8897 
    8898 > close #6
    8899 
    8900 > hide #!9 models
    8901 
    8902 > show #!9 models
    8903 
    8904 > hide #!9 models
    8905 
    8906 > show #!9 models
    8907 
    8908 > show #!12 models
    8909 
    8910 > hide #!12 models
    8911 
    8912 > hide #!15 models
    8913 
    8914 > hide #!9 models
    8915 
    8916 > show #!12 models
    8917 
    8918 > show #!9 models
    8919 
    8920 > hide #!12 models
    8921 
    8922 > show #!12 models
    8923 
    8924 > volume zone #3 nearAtoms #9,12/H-J range 5 invert true newMap true
    8925 
    8926 Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
    8927 step 1, values float32 
    8928 
    8929 > volume zone #3 nearAtoms #9,12/H-J range 4 newMap true
    8930 
    8931 Opened emd_51808.map zone as #5, grid size 500,500,500, pixel 1.35, shown at
    8932 step 1, values float32 
    8933 
    8934 > hide #!17 models
    8935 
    8936 > hide #!4 models
    8937 
    8938 > hide #!5 models
    8939 
    8940 > show #!17 models
    8941 
    8942 > hide #!17 models
    8943 
    8944 > close #17
    8945 
    8946 > show #!15 models
    8947 
    8948 > hide #!15 models
    8949 
    8950 > close #15
    8951 
    8952 > hide #!7 models
    8953 
    8954 > show #!7 models
    8955 
    8956 > show #!5 models
    8957 
    8958 > hide #!5 models
    8959 
    8960 > show #!4 models
    8961 
    8962 > hide #!4 models
    8963 
    8964 > show #!4 models
    8965 
    8966 > hide #!4 models
    8967 
    8968 > show #!5 models
    8969 
    8970 > show #!4 models
    8971 
    8972 > volume zone #3 nearAtoms #9-12/H-J range 4 newMap true
    8973 
    8974 Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
    8975 step 1, values float32 
    8976 
    8977 > hide #!7 models
    8978 
    8979 > show #!7 models
    8980 
    8981 > hide #!6 models
    8982 
    8983 > show #!6 models
    8984 
    8985 > hide #!6 models
    8986 
    8987 > hide #!4 models
    8988 
    8989 > hide #!5 models
    8990 
    8991 > hide #!7 models
    8992 
    8993 > show #!7 models
    8994 
    8995 > show #!4 models
    8996 
    8997 > hide #!4 models
    8998 
    8999 > show #!4 models
    9000 
    9001 > color #4 #fbc7c5ff models
    9002 
    9003 > color #4 #fbc7c579 models
    9004 
    9005 > hide #!4 models
    9006 
    9007 > show #!4 models
    9008 
    9009 > close #4
    9010 
    9011 > show #!5 models
    9012 
    9013 > close #5
    9014 
    9015 > show #!6 models
    9016 
    9017 > close #6
    9018 
    9019 > hide #!12 models
    9020 
    9021 > show #!12 models
    9022 
    9023 > hide #!7 models
    9024 
    9025 > show #!7 models
    9026 
    9027 > combine #9,12
    9028 
    9029 Remapping chain ID 'H' in 9h2j #12 to 'u' 
    9030 Remapping chain ID 'I' in 9h2j #12 to 'v' 
    9031 Remapping chain ID 'J' in 9h2j #12 to 'w' 
    9032 
    9033 > combine #4 name AC104x14
    9034 
    9035 > select add #5
    9036 
    9037 65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected 
    9038 
    9039 > select subtract #5
    9040 
    9041 Nothing selected 
    9042 
    9043 > select add #4
    9044 
    9045 65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected 
    9046 
    9047 > select subtract #4
    9048 
    9049 Nothing selected 
    9050 
    9051 > close #4
    9052 
    9053 > select add #5
    9054 
    9055 65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected 
    9056 
    9057 > hide #!9 models
    9058 
    9059 > hide #!12 models
    9060 
    9061 > hide #!7 models
    9062 
    9063 > show #!7 models
    9064 
    9065 > view front
    9066 
    9067 > select clear
    9068 
    9069 > volume zone #3 nearAtoms #5 range 5 invert true newMap true
    9070 
    9071 Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
    9072 step 1, values float32 
    9073 
    9074 > volume zone #3 nearAtoms #5 range 4 newMap true
    9075 
    9076 Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
    9077 step 1, values float32 
    9078 
    9079 > color #6 #cccc994d models
    9080 
    9081 > select clear
    9082 
    9083 > color #6 #cccc99ff models
    9084 
    9085 > color #6 #cccc99a1 models
    9086 
    9087 > color #6 #ff91aaff models
    9088 
    9089 > color #6 #ff91aa5e models
    9090 
    9091 > color #6 #ff91aa54 models
    9092 
    9093 > color #6 #ff91aa50 models
    9094 
    9095 > color #6 #ff91aa4e models
    9096 
    9097 > color #6 #ff91aa4c models
    9098 
    9099 > color #4 #f1f2f4ff models
    9100 
    9101 No surface chosen for hiding dust 
    9102 
    9103 > hide #!4 models
    9104 
    9105 > show #!4 models
    9106 
    9107 > surface dust #4 size 8.1
    9108 
    9109 > hide #!7 models
    9110 
    9111 > show #!7 models
    9112 
    9113 > surface dust #4 size 7.89
    9114 
    9115 > surface dust #4 size 21.25
    9116 
    9117 > volume #4 level 0.00684
    9118 
    9119 > surface dust #4 size 24.31
    9120 
    9121 > surface dust #4 size 26
    9122 
    9123 > surface dust #2 size 4.03
    9124 
    9125 > surface dust #2 size 3.96
    9126 
    9127 > surface dust #2 size 50.91
    9128 
    9129 > surface dust #2 size 43.77
    9130 
    9131 > surface dust #2 size 3.29
    9132 
    9133 > surface dust #2 size 7.13
    9134 
    9135 > surface dust #7 size 18.27
    9136 
    9137 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    9138 
    9139 ——— End of log from Wed Jun 18 01:53:42 2025 ———
    9140 
    9141 opened ChimeraX session 
    9142 
    9143 > view front
    9144 
    9145 > ui tool show "Fit in Map"
    9146 
    9147 > fitmap #12 inMap #1
    9148 
    9149 Fit molecule 9h2j (#12) to map emd_51794.map (#1) using 4686 atoms 
    9150 average map value = 0.008063, steps = 68 
    9151 shifted from previous position = 2.33 
    9152 rotated from previous position = 0.293 degrees 
    9153 atoms outside contour = 1469, contour level = 0.0064084 
    9154  
    9155 Position of 9h2j (#12) relative to emd_51794.map (#1) coordinates: 
    9156 Matrix rotation and translation 
    9157 0.91146535 -0.41137197 -0.00200365 170.21590256 
    9158 0.41135902 0.91146038 -0.00487050 -109.77073126 
    9159 0.00382984 0.00361507 0.99998613 -13.75108659 
    9160 Axis 0.01031310 -0.00708984 0.99992168 
    9161 Axis point 340.39462668 340.79827464 0.00000000 
    9162 Rotation angle (degrees) 24.29266751 
    9163 Shift along axis -11.21629888 
    9164  
    9165 
    9166 > fitmap #12 inMap #1
    9167 
    9168 Fit molecule 9h2j (#12) to map emd_51794.map (#1) using 4686 atoms 
    9169 average map value = 0.008063, steps = 44 
    9170 shifted from previous position = 0.00731 
    9171 rotated from previous position = 0.00281 degrees 
    9172 atoms outside contour = 1469, contour level = 0.0064084 
    9173  
    9174 Position of 9h2j (#12) relative to emd_51794.map (#1) coordinates: 
    9175 Matrix rotation and translation 
    9176 0.91147410 -0.41135242 -0.00203741 170.21275934 
    9177 0.41133946 0.91146936 -0.00484216 -109.78260552 
    9178 0.00384887 0.00357544 0.99998620 -13.73566446 
    9179 Axis 0.01023097 -0.00715434 0.99992207 
    9180 Axis point 340.43486206 340.80296100 0.00000000 
    9181 Rotation angle (degrees) 24.29142799 
    9182 Shift along axis -11.20773000 
    9183  
    9184 
    9185 > fitmap #12 inMap #1
    9186 
    9187 Fit molecule 9h2j (#12) to map emd_51794.map (#1) using 4686 atoms 
    9188 average map value = 0.008063, steps = 28 
    9189 shifted from previous position = 0.0382 
    9190 rotated from previous position = 0.017 degrees 
    9191 atoms outside contour = 1473, contour level = 0.0064084 
    9192  
    9193 Position of 9h2j (#12) relative to emd_51794.map (#1) coordinates: 
    9194 Matrix rotation and translation 
    9195 0.91143254 -0.41144470 -0.00199796 170.27083039 
    9196 0.41143291 0.91142860 -0.00456716 -109.87056368 
    9197 0.00370014 0.00334063 0.99998757 -13.57700929 
    9198 Axis 0.00960926 -0.00692411 0.99992986 
    9199 Axis point 340.59370619 340.78147751 0.00000000 
    9200 Rotation angle (degrees) 24.29706479 
    9201 Shift along axis -11.17912428 
    9202  
    9203 
    9204 > color #6 #ff91aa46 models
    9205 
    9206 > color #6 #ff91aa3f models
    9207 
    9208 > ui tool show "Side View"
    9209 
    9210 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2427
    9211 > supersample 4
    9212 
    9213 > color #4 #b9c2ffff models
    9214 
    9215 > color #4 #75ff79ff models
    9216 
    9217 > color #4 #f80039ff models
    9218 
    9219 > color #4 #0100f8ff models
    9220 
    9221 > color #4 #00f8efff models
    9222 
    9223 > color #4 #f8e769ff models
    9224 
    9225 > color #4 #f1f2f4ff models
    9226 
    9227 > view front
    9228 
    9229 > hide #!7 models
    9230 
    9231 > show #!7 models
    9232 
    9233 > hide #!7 models
    9234 
    9235 > show #!7 models
    9236 
    9237 > color #4 #f1f2f400 models
    9238 
    9239 > color #4 #f1f2f443 models
    9240 
    9241 > hide #!2 models
    9242 
    9243 > hide #!7 models
    9244 
    9245 > color #4 #f1f2f4ff models
    9246 
    9247 > hide #!4 models
    9248 
    9249 > show #!12 models
    9250 
    9251 > hide #!5 models
    9252 
    9253 > color #6 #ffb2c33f models
    9254 
    9255 > hide #!6 models
    9256 
    9257 > show #!9 models
    9258 
    9259 > hide #!9 models
    9260 
    9261 > show #!9 models
    9262 
    9263 > hide #!9 models
    9264 
    9265 > show #!6 models
    9266 
    9267 > show #!5 models
    9268 
    9269 > hide #!12 models
    9270 
    9271 > show #!4 models
    9272 
    9273 > lighting soft
    9274 
    9275 > lighting gentle
    9276 
    9277 > lighting simple
    9278 
    9279 > lighting full
    9280 
    9281 > lighting soft
    9282 
    9283 > lighting gentle
    9284 
    9285 > lighting soft
    9286 
    9287 > hide #!6 models
    9288 
    9289 > color #4 #f1f2f453 models
    9290 
    9291 > color #4 #f1f2f480 models
    9292 
    9293 > hide #!4 models
    9294 
    9295 > hide #!5 models
    9296 
    9297 > show #!12 models
    9298 
    9299 > view front
    9300 
    9301 > save /Users/ConstantinePetridis/Desktop/AC104.png width 4000 height 2427
    9302 > supersample 4 transparentBackground true
    9303 
    9304 > select #12/H:484
    9305 
    9306 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9307 
    9308 > select ~sel & ##selected
    9309 
    9310 4678 atoms, 4775 bonds, 4 pseudobonds, 560 residues, 2 models selected 
    9311 
    9312 > select ~sel & ##selected
    9313 
    9314 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9315 
    9316 > select up
    9317 
    9318 208 atoms, 209 bonds, 24 residues, 1 model selected 
    9319 
    9320 > select up
    9321 
    9322 1644 atoms, 1678 bonds, 196 residues, 1 model selected 
    9323 
    9324 > select up
    9325 
    9326 1652 atoms, 1685 bonds, 197 residues, 1 model selected 
    9327 
    9328 > select up
    9329 
    9330 1794 atoms, 1829 bonds, 214 residues, 1 model selected 
    9331 Alignment identifier is 12/H 
    9332 
    9333 > select clear
    9334 
    9335 > select #12/I:535
    9336 
    9337 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9338 
    9339 > select up
    9340 
    9341 74 atoms, 74 bonds, 9 residues, 1 model selected 
    9342 
    9343 > select up
    9344 
    9345 1462 atoms, 1493 bonds, 176 residues, 1 model selected 
    9346 Alignment identifier is 12/I 
    9347 
    9348 > select #12/J:569
    9349 
    9350 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9351 
    9352 > select up
    9353 
    9354 181 atoms, 185 bonds, 22 residues, 1 model selected 
    9355 
    9356 > select up
    9357 
    9358 868 atoms, 889 bonds, 103 residues, 1 model selected 
    9359 
    9360 > select up
    9361 
    9362 912 atoms, 933 bonds, 108 residues, 1 model selected 
    9363 
    9364 > select up
    9365 
    9366 1208 atoms, 1237 bonds, 144 residues, 1 model selected 
    9367 
    9368 > select up
    9369 
    9370 1266 atoms, 1295 bonds, 151 residues, 1 model selected 
    9371 
    9372 > select up
    9373 
    9374 1430 atoms, 1460 bonds, 171 residues, 1 model selected 
    9375 Alignment identifier is 12/J 
    9376 
    9377 > select clear
    9378 
    9379 > open
    9380 > /Users/ConstantinePetridis/Downloads/fold_2025_06_15_21_59_vp80/fold_2025_06_15_21_59_vp80_model_0.cif
    9381 
    9382 Chain information for fold_2025_06_15_21_59_vp80_model_0.cif #8 
    9383 --- 
    9384 Chain | Description 
    9385 A | . 
    9386  
    9387 Computing secondary structure 
    9388 
    9389 > hide #!12 models
    9390 
    9391 > select add #8
    9392 
    9393 5609 atoms, 5698 bonds, 691 residues, 1 model selected 
    9394 
    9395 > view sel
    9396 
    9397 > select clear
    9398 
    9399 > open
    9400 > /Users/ConstantinePetridis/Downloads/fold_2025_06_15_21_59_vp80/fold_2025_06_15_21_59_vp80_model_1.cif
    9401 
    9402 Chain information for fold_2025_06_15_21_59_vp80_model_1.cif #10 
    9403 --- 
    9404 Chain | Description 
    9405 A | . 
    9406  
    9407 Computing secondary structure 
    9408 
    9409 > hide #8 models
    9410 
    9411 > show #8 models
    9412 
    9413 > hide #10 models
    9414 
    9415 > graphics silhouettes width 2.1
    9416 
    9417 > cartoon style protein modeHelix tube radius 1.9 sides 24
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    9419 > color #8 #f1f2f4ff
    9420 
    9421 > select #8/462-690
    9422 
    9423 Nothing selected 
    9424 
    9425 > hide #8 models
    9426 
    9427 > show #8 models
    9428 
    9429 > select #8/A:462-690
    9430 
    9431 1917 atoms, 1954 bonds, 229 residues, 1 model selected 
    9432 
    9433 > color sel #ff91aaff
    9434 
    9435 > color sel #f34d8fff
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    9437 > color sel #ff91aaff
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    9475 > select clear
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    9479 Nothing selected 
    9480 
    9481 > select #8/A:424-239
    9482 
    9483 Nothing selected 
    9484 
    9485 > select #8/A:424-439
    9486 
    9487 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9488 
    9489 > surface sel
    9490 
    9491 > select clear
    9492 
    9493 > select #8/A:424-439
    9494 
    9495 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9496 
    9497 > color #8 #f1f2f4ae
    9498 
    9499 > color #8 #f1f2f4ff
    9500 
    9501 > undo
    9502 
    9503 > select clear
    9504 
    9505 > select #8/A:424-439
    9506 
    9507 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9508 
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    9593 > color (#!8 & sel) #75ff7980
    9594 
    9595 > select clear
    9596 
    9597 > select #8/A
    9598 
    9599 5609 atoms, 5698 bonds, 691 residues, 1 model selected 
    9600 
    9601 > color (#!8 & sel) #75ff7980
    9602 
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    9620 
    9621 > color (#!8 & sel) #f1f2f4ff
    9622 
    9623 > select #8/A:424-439
    9624 
    9625 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9626 
    9627 > color (#!8 & sel) #75ff79ff
    9628 
    9629 > color (#!8 & sel) #75ff79fb
    9630 
    9631 > color (#!8 & sel) #75ff79e5
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    9761 > select clear
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    9763 > hide #!8 surfaces
    9764 
    9765 > select clear
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    9777 > select clear
    9778 
    9779 > select #8/A:424-439
    9780 
    9781 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9782 
    9783 > color (#!8 & sel) #75ff79ff
    9784 
    9785 > select clear
    9786 
    9787 > color #8 #91f88cff
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    9789 > color #8 #91f88bff
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    9801 > color #8 #8bf880ff
    9802 
    9803 > color #8 #f1f2f4ff
    9804 
    9805 > select #8/A:424-439
    9806 
    9807 129 atoms, 129 bonds, 16 residues, 1 model selected 
    9808 
    9809 > color (#!8 & sel) #eaf6e6ff
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    9843 > color (#!8 & sel) #29f600ff
    9844 
    9845 > select clear
    9846 
    9847 > select #8/A:462-690
    9848 
    9849 1917 atoms, 1954 bonds, 229 residues, 1 model selected 
    9850 
    9851 > color (#!8 & sel) #ff91aaff
    9852 
    9853 > color (#!8 & sel) #ff92adff
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    9855 > color (#!8 & sel) #fc91abff
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    9904 
    9905 > select clear
    9906 
    9907 > select #8/A:424-439
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    9909 129 atoms, 129 bonds, 16 residues, 1 model selected 
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    10073 > color (#!8 & sel) #e8a00cff
    10074 
    10075 > color (#!8 & sel) #e8a111ff
    10076 
    10077 > color (#!8 & sel) #e8a932ff
    10078 
    10079 > color (#!8 & sel) #e8aa61ff
    10080 
    10081 > color (#!8 & sel) #e89782ff
    10082 
    10083 > color (#!8 & sel) #e88495ff
    10084 
    10085 > color (#!8 & sel) #e86db8ff
    10086 
    10087 > color (#!8 & sel) #e83edcff
    10088 
    10089 > color (#!8 & sel) #e428e8ff
    10090 
    10091 > color (#!8 & sel) #dc1de8ff
    10092 
    10093 > color (#!8 & sel) #d819e8ff
    10094 
    10095 > color (#!8 & sel) #d414e8ff
    10096 
    10097 > color (#!8 & sel) #d211e8ff
    10098 
    10099 > color (#!8 & sel) #d00fe8ff
    10100 
    10101 > color (#!8 & sel) #cf0ee8ff
    10102 
    10103 > color (#!8 & sel) #ce0de8ff
    10104 
    10105 > color (#!8 & sel) #cd0be8ff
    10106 
    10107 > color (#!8 & sel) #c807e8ff
    10108 
    10109 > color (#!8 & sel) #c300e8ff
    10110 
    10111 > color (#!8 & sel) #c000e8ff
    10112 
    10113 > color (#!8 & sel) #c100e8ff
    10114 
    10115 > color (#!8 & sel) #bf00e8ff
    10116 
    10117 > color (#!8 & sel) #be00e8ff
    10118 
    10119 > color (#!8 & sel) #bc00e8ff
    10120 
    10121 > color (#!8 & sel) #ba00e8ff
    10122 
    10123 > color (#!8 & sel) #b30be8ff
    10124 
    10125 > color (#!8 & sel) #ab20e8ff
    10126 
    10127 > color (#!8 & sel) #993ae8ff
    10128 
    10129 > color (#!8 & sel) #784ce8ff
    10130 
    10131 > color (#!8 & sel) #6350e8ff
    10132 
    10133 > color (#!8 & sel) #4f57e8ff
    10134 
    10135 > color (#!8 & sel) #4570e8ff
    10136 
    10137 > color (#!8 & sel) #377fe8ff
    10138 
    10139 > color (#!8 & sel) #2a86e8ff
    10140 
    10141 > color (#!8 & sel) #178fe8ff
    10142 
    10143 > color (#!8 & sel) #0e91e8ff
    10144 
    10145 > color (#!8 & sel) #0a91e8ff
    10146 
    10147 > color (#!8 & sel) #0592e8ff
    10148 
    10149 > color (#!8 & sel) #0293e8ff
    10150 
    10151 > color (#!8 & sel) #0095e8ff
    10152 
    10153 > color (#!8 & sel) #0096e8ff
    10154 
    10155 > color (#!8 & sel) #0098e8ff
    10156 
    10157 > color (#!8 & sel) #009ae8ff
    10158 
    10159 > color (#!8 & sel) #009fe8ff
    10160 
    10161 > color (#!8 & sel) #00a1e8ff
    10162 
    10163 > color (#!8 & sel) #00a3e8ff
    10164 
    10165 > color (#!8 & sel) #00a4e8ff
    10166 
    10167 > color (#!8 & sel) #00a6e8ff
    10168 
    10169 > color (#!8 & sel) #00a8e8ff
    10170 
    10171 > color (#!8 & sel) #00aae8ff
    10172 
    10173 > color (#!8 & sel) #00abe8ff
    10174 
    10175 > color (#!8 & sel) #00ade8ff
    10176 
    10177 > color (#!8 & sel) #00abe8ff
    10178 
    10179 > color (#!8 & sel) #00a1e8ff
    10180 
    10181 > color (#!8 & sel) #0093e8ff
    10182 
    10183 > color (#!8 & sel) #0385e8ff
    10184 
    10185 > color (#!8 & sel) #0a82e8ff
    10186 
    10187 > color (#!8 & sel) #0e80e8ff
    10188 
    10189 > color (#!8 & sel) #147ee8ff
    10190 
    10191 > color (#!8 & sel) #197de8ff
    10192 
    10193 > color (#!8 & sel) #1f7ce8ff
    10194 
    10195 > color (#!8 & sel) #1f7be8ff
    10196 
    10197 > color (#!8 & sel) #1f7ae8ff
    10198 
    10199 > color (#!8 & sel) #1873e8ff
    10200 
    10201 > color (#!8 & sel) #0f6ae8ff
    10202 
    10203 > color (#!8 & sel) #0862e8ff
    10204 
    10205 > color (#!8 & sel) #035de8ff
    10206 
    10207 > color (#!8 & sel) #0059e8ff
    10208 
    10209 > color (#!8 & sel) #0055e8ff
    10210 
    10211 > color (#!8 & sel) #0054e8ff
    10212 
    10213 > color (#!8 & sel) #0152e8ff
    10214 
    10215 > color (#!8 & sel) #004ce8ff
    10216 
    10217 > color (#!8 & sel) #0046e8ff
    10218 
    10219 > color (#!8 & sel) #0045e8ff
    10220 
    10221 > color (#!8 & sel) #0043e8ff
    10222 
    10223 > color (#!8 & sel) #0045e8ff
    10224 
    10225 > color (#!8 & sel) #0043e8ff
    10226 
    10227 > color (#!8 & sel) #0045e8ff
    10228 
    10229 > color (#!8 & sel) #0043e8ff
    10230 
    10231 > color (#!8 & sel) #0042e8ff
    10232 
    10233 > color (#!8 & sel) #003ee8ff
    10234 
    10235 > color (#!8 & sel) #1849e8ff
    10236 
    10237 > color (#!8 & sel) #4b66e8ff
    10238 
    10239 > color (#!8 & sel) #777de8ff
    10240 
    10241 > color (#!8 & sel) #8a89e8ff
    10242 
    10243 > color (#!8 & sel) #a19be8ff
    10244 
    10245 > color (#!8 & sel) #a39de8ff
    10246 
    10247 > color (#!8 & sel) #a49de8ff
    10248 
    10249 > color (#!8 & sel) #a59ee8ff
    10250 
    10251 > color (#!8 & sel) #afa4e8ff
    10252 
    10253 > color (#!8 & sel) #c2aee8ff
    10254 
    10255 > color (#!8 & sel) #d7b7e8ff
    10256 
    10257 > color (#!8 & sel) #dbb8e8ff
    10258 
    10259 > color (#!8 & sel) #dcb8e8ff
    10260 
    10261 > color (#!8 & sel) #dfb9e8ff
    10262 
    10263 > color (#!8 & sel) #e8bae5ff
    10264 
    10265 > color (#!8 & sel) #e8b6d0ff
    10266 
    10267 > color (#!8 & sel) #e8afc2ff
    10268 
    10269 > color (#!8 & sel) #e8a1a9ff
    10270 
    10271 > color (#!8 & sel) #e89791ff
    10272 
    10273 > color (#!8 & sel) #e89283ff
    10274 
    10275 > color (#!8 & sel) #e88d76ff
    10276 
    10277 > color (#!8 & sel) #e8896aff
    10278 
    10279 > color (#!8 & sel) #e88762ff
    10280 
    10281 > color (#!8 & sel) #e8845aff
    10282 
    10283 > color (#!8 & sel) #e88256ff
    10284 
    10285 > color (#!8 & sel) #e88153ff
    10286 
    10287 > color (#!8 & sel) #e88152ff
    10288 
    10289 > color (#!8 & sel) #e8804eff
    10290 
    10291 > color (#!8 & sel) #e87f4cff
    10292 
    10293 > color (#!8 & sel) #e87f4bff
    10294 
    10295 > color (#!8 & sel) #e87f49ff
    10296 
    10297 > color (#!8 & sel) #e87c41ff
    10298 
    10299 > color (#!8 & sel) #e87b3cff
    10300 
    10301 > color (#!8 & sel) #e87730ff
    10302 
    10303 > color (#!8 & sel) #e8762bff
    10304 
    10305 > color (#!8 & sel) #e87525ff
    10306 
    10307 > color (#!8 & sel) #e8741cff
    10308 
    10309 > color (#!8 & sel) #e87215ff
    10310 
    10311 > color (#!8 & sel) #e87211ff
    10312 
    10313 > color (#!8 & sel) #e8700cff
    10314 
    10315 > color (#!8 & sel) #e8700aff
    10316 
    10317 > color (#!8 & sel) #e87009ff
    10318 
    10319 > color (#!8 & sel) #e87008ff
    10320 
    10321 > color (#!8 & sel) #75ff79ff
    10322 
    10323 > color (#!8 & sel) #9df88fff
    10324 
    10325 > color (#!8 & sel) #9bf88cff
    10326 
    10327 > color (#!8 & sel) #8af877ff
    10328 
    10329 > color (#!8 & sel) #7cf868ff
    10330 
    10331 > color (#!8 & sel) #64f84eff
    10332 
    10333 > color (#!8 & sel) #55f83cff
    10334 
    10335 > color (#!8 & sel) #4cf832ff
    10336 
    10337 > color (#!8 & sel) #47f82aff
    10338 
    10339 > color (#!8 & sel) #44f826ff
    10340 
    10341 > color (#!8 & sel) #42f823ff
    10342 
    10343 > color (#!8 & sel) #3cf81eff
    10344 
    10345 > color (#!8 & sel) #31f80fff
    10346 
    10347 > color (#!8 & sel) #2af808ff
    10348 
    10349 > color (#!8 & sel) #25f803ff
    10350 
    10351 > color (#!8 & sel) #27f800ff
    10352 
    10353 > color (#!8 & sel) #29f800ff
    10354 
    10355 > color (#!8 & sel) #27f800ff
    10356 
    10357 > select clear
    10358 
    10359 > select #8/A:469-472
    10360 
    10361 40 atoms, 39 bonds, 4 residues, 1 model selected 
    10362 
    10363 > color (#!8 & sel) #213af8ff
    10364 
    10365 > color (#!8 & sel) #203af8ff
    10366 
    10367 > color (#!8 & sel) #1936f8ff
    10368 
    10369 > color (#!8 & sel) #1633f8ff
    10370 
    10371 > color (#!8 & sel) #1130f8ff
    10372 
    10373 > color (#!8 & sel) #0e2ff8ff
    10374 
    10375 > color (#!8 & sel) #0b2cf8ff
    10376 
    10377 > color (#!8 & sel) #082bf8ff
    10378 
    10379 > color (#!8 & sel) #0428f8ff
    10380 
    10381 > color (#!8 & sel) #0126f8ff
    10382 
    10383 > color (#!8 & sel) #0026f8ff
    10384 
    10385 > color (#!8 & sel) #0027f8ff
    10386 
    10387 > color (#!8 & sel) #002af8ff
    10388 
    10389 > color (#!8 & sel) #002cf8ff
    10390 
    10391 > color (#!8 & sel) #002ef8ff
    10392 
    10393 > color (#!8 & sel) #002ff8ff
    10394 
    10395 > color (#!8 & sel) #0031f8ff
    10396 
    10397 > select clear
    10398 
    10399 > save /Users/ConstantinePetridis/Desktop/AC104-2.png width 4000 height 2427
    10400 > supersample 4
    10401 
    10402 > save /Users/ConstantinePetridis/Desktop/AC104-2.png width 4000 height 2427
    10403 > supersample 4 transparentBackground true
    10404 
    10405 > lighting soft
    10406 
    10407 > lighting gentle
    10408 
    10409 > lighting soft
    10410 
    10411 > show #!12 models
    10412 
    10413 > hide #!8 models
    10414 
    10415 > view #12 clip false
    10416 
    10417 
    10418 ===== Log before crash end =====
    10419 
    10420 Log:
    10421 UCSF ChimeraX version: 1.9 (2024-12-11) 
    10422 © 2016-2024 Regents of the University of California. All rights reserved. 
    10423 
    10424 > open /Users/ConstantinePetridis/Desktop/BVcap.cxs
    10425 
    10426 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10427 0.00641, step 1, values float32 
    10428 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10429 0.00819, step 1, values float32 
    10430 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10431 0.00742, step 1, values float32 
    10432 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10433 0.00667, step 1, values float32 
    10434 Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
    10435 level 0.00684, step 1, values float32 
    10436 Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
    10437 level 0.00742, step 1, values float32 
    10438 Log from Wed Jun 18 01:53:42 2025UCSF ChimeraX version: 1.9 (2024-12-11) 
    10439 © 2016-2024 Regents of the University of California. All rights reserved. 
    10440 
    10441 > open /Users/ConstantinePetridis/Desktop/BVcap.cxs
    10442 
    10443 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10444 0.00641, step 1, values float32 
    10445 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10446 0.00819, step 1, values float32 
    10447 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10448 0.00742, step 1, values float32 
    10449 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10450 0.00667, step 1, values float32 
    10451 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    10452 level 0.00705, step 1, values float32 
    10453 Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
    10454 level 0.00742, step 1, values float32 
    10455 Opened emd_51808.map zone as #9, grid size 500,500,500, pixel 1.35, shown at
    10456 level 0.00742, step 1, values float32 
    10457 Log from Wed Jun 18 01:06:40 2025UCSF ChimeraX version: 1.9 (2024-12-11) 
    10458 © 2016-2024 Regents of the University of California. All rights reserved. 
    10459 
    10460 > open /Users/ConstantinePetridis/Desktop/BVcap.cxs
    10461 
    10462 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10463 0.00641, step 1, values float32 
    10464 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10465 0.00819, step 1, values float32 
    10466 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10467 0.00742, step 1, values float32 
    10468 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10469 0.00667, step 1, values float32 
    10470 Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
    10471 level 0.00705, step 1, values float32 
    10472 Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
    10473 level 0.00742, step 1, values float32 
    10474 Log from Sun Jun 15 21:01:47 2025UCSF ChimeraX version: 1.9 (2024-12-11) 
    10475 © 2016-2024 Regents of the University of California. All rights reserved. 
    10476 
    10477 > open /Users/ConstantinePetridis/Desktop/BVcap.cxs
    10478 
    10479 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10480 0.00641, step 1, values float32 
    10481 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10482 0.00819, step 1, values float32 
    10483 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10484 0.00742, step 1, values float32 
    10485 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10486 0.00667, step 1, values float32 
    10487 Log from Mon Jun 9 23:00:16 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    10488 © 2016-2024 Regents of the University of California. All rights reserved. 
    10489 
    10490 > open /Users/ConstantinePetridis/Desktop/BVcap.cxs format session
    10491 
    10492 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10493 0.00641, step 1, values float32 
    10494 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10495 0.00819, step 1, values float32 
    10496 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10497 0.00742, step 1, values float32 
    10498 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10499 0.00667, step 1, values float32 
    10500 Log from Mon Jun 9 21:58:32 2025 Startup Messages 
    10501 --- 
    10502 warning | Registration file '/Users/ConstantinePetridis/Library/Application Support/ChimeraX/registration' has expired 
    10503 note | available bundle cache has not been initialized yet 
    10504  
    10505 You can double click a model's Name or ID in the model panel to edit those
    10506 fields 
    10507 UCSF ChimeraX version: 1.8 (2024-06-10) 
    10508 © 2016-2024 Regents of the University of California. All rights reserved. 
    10509 How to cite UCSF ChimeraX 
    10510 
    10511 > open /Users/ConstantinePetridis/Downloads/emd_51794.map
    10512 
    10513 Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
    10514 0.00783, step 2, values float32 
    10515 
    10516 > ui tool show Registration
    10517 
    10518 Thank you for registering your copy of ChimeraX. By providing the information
    10519 requested you will be helping us document the impact this software is having
    10520 in the scientific community. The information you supplied will only be used
    10521 for reporting summary usage statistics; no individual data will be released. 
    10522 petridis@mit.edu has been invited to the ChimeraX announcements list 
    10523 
    10524 > volume #1 step 1
    10525 
    10526 > volume #1 level 0.006408
    10527 
    10528 > open /Users/ConstantinePetridis/Downloads/emd_51809.map
    10529 
    10530 Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
    10531 0.00787, step 2, values float32 
    10532 
    10533 > open /Users/ConstantinePetridis/Downloads/emd_51808.map
    10534 
    10535 Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
    10536 0.00734, step 2, values float32 
    10537 
    10538 > select add #2
    10539 
    10540 2 models selected 
    10541 
    10542 > ui mousemode right "translate selected models"
    10543 
    10544 > view matrix models #2,1,0,0,108.6,0,1,0,134.66,0,0,1,242.83
    10545 
    10546 > view matrix models #2,1,0,0,132.26,0,1,0,134.39,0,0,1,239.35
    10547 
    10548 > view matrix models #2,1,0,0,133.6,0,1,0,135.11,0,0,1,235.01
    10549 
    10550 > select clear
    10551 
    10552 > open 9H2J, 9H2K, 9H2H
    10553 
    10554 '9H2J,' has no suffix 
    10555 
    10556 > open 9H2J
    10557 
    10558 Summary of feedback from opening 9H2J fetched from pdb 
    10559 --- 
    10560 notes | Fetching compressed mmCIF 9h2j from http://files.rcsb.org/download/9h2j.cif 
    10561 Fetching CCD ZN from
    10562 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 
    10563  
    10564 9h2j title: 
    10565 AcMNPV apical cap - C14 anchor complex only [more info...] 
    10566  
    10567 Chain information for 9h2j #4 
    10568 --- 
    10569 Chain | Description | UniProt 
    10570 A B | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 
    10571 C D | Protein C42 | C42_NPVAC 1-361 
    10572 E | Protein AC142 | AC142_NPVAC 1-477 
    10573 F G L M | Major capsid protein | MCP_NPVAC 1-347 
    10574 H I J | Capsid-associated protein VP80 | VP80_NPVAC 1-691 
    10575 K | Protein AC109 | AC109_NPVAC 1-390 
    10576 N P | Protein Ac66 | AC66_NPVAC 1-808 
    10577 O | Tyrosine-protein phosphatase | PTP_NPVAC 1-168 
    10578  
    10579 Non-standard residues in 9h2j #4 
    10580 --- 
    10581 ZN — zinc ion 
    10582  
    10583 9h2j mmCIF Assemblies 
    10584 --- 
    10585 1| author_defined_assembly 
    10586  
    10587 
    10588 > open 9H2K
    10589 
    10590 Summary of feedback from opening 9H2K fetched from pdb 
    10591 --- 
    10592 note | Fetching compressed mmCIF 9h2k from http://files.rcsb.org/download/9h2k.cif 
    10593  
    10594 9h2k title: 
    10595 AcMNPV apical cap - C21 ring [more info...] 
    10596  
    10597 Chain information for 9h2k #5 
    10598 --- 
    10599 Chain | Description | UniProt 
    10600 A B | Protein Ac66 | AC66_NPVAC 1-808 
    10601 C E | Protein Ac102 | AC102_NPVAC 1-122 
    10602 D F | Protein C42 | C42_NPVAC 1-361 
    10603  
    10604 9h2k mmCIF Assemblies 
    10605 --- 
    10606 1| author_defined_assembly 
    10607  
    10608 
    10609 > open 9H2H
    10610 
    10611 Summary of feedback from opening 9H2H fetched from pdb 
    10612 --- 
    10613 note | Fetching compressed mmCIF 9h2h from http://files.rcsb.org/download/9h2h.cif 
    10614  
    10615 9h2h title: 
    10616 AcMNPV apical cap - composite map of the C2 plug [more info...] 
    10617  
    10618 Chain information for 9h2h #6 
    10619 --- 
    10620 Chain | Description | UniProt 
    10621 A B C D | Protein AC54 | AC54_NPVAC 1-365 
    10622 E | DNA (58-MER) |   
    10623 F | DNA (58-MER) |   
    10624 G H K L O P S T | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 
    10625 I J M N Q R U V | Protein C42 | C42_NPVAC 1-361 
    10626  
    10627 9h2h mmCIF Assemblies 
    10628 --- 
    10629 1| author_and_software_defined_assembly 
    10630  
    10631 
    10632 > show cartoons
    10633 
    10634 > hide atoms
    10635 
    10636 > transparency #1-3, 50
    10637 
    10638 Missing or invalid "percent" argument: Expected a number 
    10639 
    10640 > transparency #1-3 50
    10641 
    10642 > select add #4
    10643 
    10644 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    10645 
    10646 > view matrix models #4,1,0,0,-46.281,0,1,0,28.188,0,0,1,16.931
    10647 
    10648 > view matrix models #4,1,0,0,-66.8,0,1,0,31.821,0,0,1,22.566
    10649 
    10650 > view matrix models #4,1,0,0,-83.932,0,1,0,-4.1614,0,0,1,3.3295
    10651 
    10652 > view matrix models #4,1,0,0,-86.753,0,1,0,-14.247,0,0,1,2.2438
    10653 
    10654 > ui mousemode right "rotate selected models"
    10655 
    10656 > view matrix models
    10657 > #4,0.98834,-0.084105,-0.12696,3.7899,0.12496,0.9244,0.36038,-157.79,0.087054,-0.37204,0.92413,172.5
    10658 
    10659 > ui tool show "Fit in Map"
    10660 
    10661 > fitmap #4 inMap #1
    10662 
    10663 Fit molecule 9h2j (#4) to map emd_51794.map (#1) using 28099 atoms 
    10664 average map value = 0.00362, steps = 208 
    10665 shifted from previous position = 16.5 
    10666 rotated from previous position = 26.1 degrees 
    10667 atoms outside contour = 20539, contour level = 0.0064084 
    10668  
    10669 Position of 9h2j (#4) relative to emd_51794.map (#1) coordinates: 
    10670 Matrix rotation and translation 
    10671 0.87093476 0.22125067 -0.43877191 8.17307974 
    10672 -0.03651218 0.91957262 0.39121997 -98.27311021 
    10673 0.49004032 -0.32470655 0.80896610 9.06190185 
    10674 Axis -0.59625676 -0.77355784 -0.21467684 
    10675 Axis point -4.38407802 0.00000000 113.95591535 
    10676 Rotation angle (degrees) 36.89503018 
    10677 Shift along axis 69.20130055 
    10678  
    10679 
    10680 > undo
    10681 
    10682 > fitmap #4 inMap #2
    10683 
    10684 Fit molecule 9h2j (#4) to map emd_51809.map (#2) using 28099 atoms 
    10685 average map value = 0.0009505, steps = 2000 
    10686 shifted from previous position = 32.2 
    10687 rotated from previous position = 19.8 degrees 
    10688 atoms outside contour = 26476, contour level = 0.0078685 
    10689  
    10690 Position of 9h2j (#4) relative to emd_51809.map (#2) coordinates: 
    10691 Matrix rotation and translation 
    10692 0.97206708 -0.20356372 -0.11682209 -57.64338192 
    10693 0.16794355 0.95098530 -0.25965733 -117.85047834 
    10694 0.16395290 0.23278483 0.95860872 -372.18017582 
    10695 Axis 0.72657867 -0.41427224 0.54814409 
    10696 Axis point 0.00000000 965.75111056 -950.58571178 
    10697 Rotation angle (degrees) 19.80849290 
    10698 Shift along axis -197.06863558 
    10699  
    10700 
    10701 > undo
    10702 
    10703 > fitmap #4 inMap #3
    10704 
    10705 Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms 
    10706 average map value = 0.008828, steps = 240 
    10707 shifted from previous position = 23.3 
    10708 rotated from previous position = 25.7 degrees 
    10709 atoms outside contour = 12094, contour level = 0.0073443 
    10710  
    10711 Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates: 
    10712 Matrix rotation and translation 
    10713 0.90107510 -0.43366308 -0.00001525 179.72189974 
    10714 0.43366305 0.90107502 0.00041028 -113.14051793 
    10715 -0.00016418 -0.00037631 0.99999992 0.26283972 
    10716 Axis -0.00090692 0.00017172 0.99999957 
    10717 Axis point 337.85156358 337.35875693 0.00000000 
    10718 Rotation angle (degrees) 25.70026512 
    10719 Shift along axis 0.08041870 
    10720  
    10721 
    10722 > open /Users/ConstantinePetridis/Downloads/emd_51803.map
    10723 
    10724 Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
    10725 0.00751, step 2, values float32 
    10726 
    10727 > select add #1
    10728 
    10729 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 5 models selected 
    10730 
    10731 > select subtract #4
    10732 
    10733 2 models selected 
    10734 
    10735 > select add #7
    10736 
    10737 4 models selected 
    10738 
    10739 > select subtract #1
    10740 
    10741 2 models selected 
    10742 
    10743 > view matrix models
    10744 > #7,0.63982,-0.76148,0.10384,203.6,0.69653,0.63166,0.34036,-143.59,-0.32477,-0.14544,0.93454,110.05
    10745 
    10746 > ui mousemode right "translate selected models"
    10747 
    10748 > view matrix models
    10749 > #7,0.63982,-0.76148,0.10384,323.48,0.69653,0.63166,0.34036,12.879,-0.32477,-0.14544,0.93454,319.53
    10750 
    10751 > view matrix models
    10752 > #7,0.63982,-0.76148,0.10384,325.29,0.69653,0.63166,0.34036,-6.3507,-0.32477,-0.14544,0.93454,323.74
    10753 
    10754 > view matrix models
    10755 > #7,0.63982,-0.76148,0.10384,328.74,0.69653,0.63166,0.34036,-27.175,-0.32477,-0.14544,0.93454,313.1
    10756 
    10757 > view matrix models
    10758 > #7,0.63982,-0.76148,0.10384,337.59,0.69653,0.63166,0.34036,-5.7431,-0.32477,-0.14544,0.93454,280.28
    10759 
    10760 > ui mousemode right "rotate selected models"
    10761 
    10762 > view matrix models
    10763 > #7,0.67081,-0.73895,-0.062905,364.54,0.73898,0.67317,-0.027473,60.615,0.062647,-0.028056,0.99764,163.76
    10764 
    10765 > ui mousemode right "translate selected models"
    10766 
    10767 > view matrix models
    10768 > #7,0.67081,-0.73895,-0.062905,368.43,0.73898,0.67317,-0.027473,62.379,0.062647,-0.028056,0.99764,142.56
    10769 
    10770 > fitmap #2 inMap #1
    10771 
    10772 Fit map emd_51809.map in map emd_51794.map using 33729 points 
    10773 correlation = 0.9005, correlation about mean = 0.1465, overlap = 2.248 
    10774 steps = 96, shift = 1.01, angle = 4 degrees 
    10775  
    10776 Position of emd_51809.map (#2) relative to emd_51794.map (#1) coordinates: 
    10777 Matrix rotation and translation 
    10778 0.99756036 0.06957153 0.00575640 119.32853341 
    10779 -0.06957467 0.99757669 0.00034690 148.86563940 
    10780 -0.00571832 -0.00074655 0.99998337 236.80790602 
    10781 Axis -0.00783142 0.08218369 -0.99658643 
    10782 Axis point 2460.92883154 -1603.60164279 0.00000000 
    10783 Rotation angle (degrees) 4.00315534 
    10784 Shift along axis -224.69973002 
    10785  
    10786 
    10787 > fitmap #3 inMap #1
    10788 
    10789 Fit map emd_51808.map in map emd_51794.map using 156145 points 
    10790 correlation = 0.9651, correlation about mean = 0.5761, overlap = 15.43 
    10791 steps = 76, shift = 10.1, angle = 1.69 degrees 
    10792  
    10793 Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates: 
    10794 Matrix rotation and translation 
    10795 0.99956547 0.02947662 0.00000307 -9.80341163 
    10796 -0.02947662 0.99956547 -0.00000496 10.09674613 
    10797 -0.00000322 0.00000487 1.00000000 -10.09636804 
    10798 Axis 0.00016671 0.00010665 -0.99999998 
    10799 Axis point 337.52062125 337.61534124 0.00000000 
    10800 Rotation angle (degrees) 1.68913034 
    10801 Shift along axis 10.09581033 
    10802  
    10803 
    10804 > fitmap #7 inMap #1
    10805 
    10806 Fit map emd_51803.map in map emd_51794.map using 33716 points 
    10807 correlation = 0.8122, correlation about mean = -0.01378, overlap = 1.663 
    10808 steps = 160, shift = 25.9, angle = 4.23 degrees 
    10809  
    10810 Position of emd_51803.map (#7) relative to emd_51794.map (#1) coordinates: 
    10811 Matrix rotation and translation 
    10812 0.69259058 -0.72133091 0.00000784 343.32114170 
    10813 0.72133091 0.69259058 -0.00003116 51.18973084 
    10814 0.00001704 0.00002724 1.00000000 123.95738155 
    10815 Axis 0.00004048 -0.00000638 1.00000000 
    10816 Axis point 111.59922295 428.38794901 0.00000000 
    10817 Rotation angle (degrees) 46.16447282 
    10818 Shift along axis 123.97095287 
    10819  
    10820 
    10821 > hide #!1 models
    10822 
    10823 > transparency #1-3,7 50
    10824 
    10825 > select #3
    10826 
    10827 2 models selected 
    10828 
    10829 > select clear
    10830 
    10831 > select add #4
    10832 
    10833 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    10834 
    10835 > select subtract #4
    10836 
    10837 Nothing selected 
    10838 
    10839 > select add #5
    10840 
    10841 3455 atoms, 3509 bonds, 440 residues, 1 model selected 
    10842 
    10843 > view matrix models #5,1,0,0,114.4,0,1,0,365.93,0,0,1,111.77
    10844 
    10845 > view matrix models #5,1,0,0,240.9,0,1,0,294.24,0,0,1,221.01
    10846 
    10847 > view matrix models #5,1,0,0,174.7,0,1,0,215.04,0,0,1,317.11
    10848 
    10849 > view matrix models #5,1,0,0,232.67,0,1,0,162.63,0,0,1,266.73
    10850 
    10851 > view matrix models #5,1,0,0,165.64,0,1,0,140.42,0,0,1,259.08
    10852 
    10853 > view matrix models #5,1,0,0,165.46,0,1,0,122.68,0,0,1,250.56
    10854 
    10855 > view matrix models #5,1,0,0,165.79,0,1,0,135.68,0,0,1,235.75
    10856 
    10857 > fitmap #5 inMap #2
    10858 
    10859 Fit molecule 9h2k (#5) to map emd_51809.map (#2) using 3455 atoms 
    10860 average map value = 0.01384, steps = 116 
    10861 shifted from previous position = 5.06 
    10862 rotated from previous position = 21.1 degrees 
    10863 atoms outside contour = 1068, contour level = 0.0078685 
    10864  
    10865 Position of 9h2k (#5) relative to emd_51809.map (#2) coordinates: 
    10866 Matrix rotation and translation 
    10867 0.95550286 0.29498139 -0.00051665 -50.65330010 
    10868 -0.29498151 0.95550295 -0.00016089 68.77024810 
    10869 0.00044620 0.00030613 0.99999985 -0.15799858 
    10870 Axis 0.00079160 -0.00163204 -0.99999835 
    10871 Axis point 202.62055632 202.28170834 0.00000000 
    10872 Rotation angle (degrees) 17.15645426 
    10873 Shift along axis 0.00566547 
    10874  
    10875 
    10876 > select add #6
    10877 
    10878 42553 atoms, 43579 bonds, 214 pseudobonds, 5031 residues, 4 models selected 
    10879 
    10880 > select subtract #5
    10881 
    10882 39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected 
    10883 
    10884 > view matrix models #6,1,0,0,10.171,0,1,0,142.23,0,0,1,166.79
    10885 
    10886 > view matrix models #6,1,0,0,126.84,0,1,0,137.47,0,0,1,159.59
    10887 
    10888 > fitmap #6 inMap #7
    10889 
    10890 Fit molecule 9h2h (#6) to map emd_51803.map (#7) using 39098 atoms 
    10891 average map value = 0.005833, steps = 248 
    10892 shifted from previous position = 37.9 
    10893 rotated from previous position = 5.12 degrees 
    10894 atoms outside contour = 26889, contour level = 0.0075068 
    10895  
    10896 Position of 9h2h (#6) relative to emd_51803.map (#7) coordinates: 
    10897 Matrix rotation and translation 
    10898 0.71322674 0.69985623 -0.03884423 -74.42080862 
    10899 -0.70048731 0.70970069 -0.07511631 214.67231818 
    10900 -0.02500284 0.08078485 0.99641792 -14.36437549 
    10901 Axis 0.11064171 -0.00982312 -0.99381181 
    10902 Axis point 224.12956068 198.79839136 0.00000000 
    10903 Rotation angle (degrees) 44.79171059 
    10904 Shift along axis 3.93268849 
    10905  
    10906 
    10907 > select clear
    10908 
    10909 > transparency #1-3,7 30
    10910 
    10911 > transparency #1-3,7 70
    10912 
    10913 > select #4/A,B
    10914 
    10915 3475 atoms, 3533 bonds, 7 pseudobonds, 428 residues, 2 models selected 
    10916 
    10917 > select #4/A-D<H-J
    10918 
    10919 Expected an objects specifier or a keyword 
    10920 
    10921 > select #4/A-D,H-J
    10922 
    10923 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10924 
    10925 > color (#!4 & sel) red
    10926 
    10927 > select #4/A-D,H-J
    10928 
    10929 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10930 
    10931 > select #5/D,F
    10932 
    10933 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    10934 
    10935 > select #6/G-V
    10936 
    10937 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    10938 
    10939 > color (#!6 & sel) red
    10940 
    10941 > select #4/A-D,H-J
    10942 
    10943 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10944 
    10945 > select #5/D,F
    10946 
    10947 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    10948 
    10949 > select #6/G-V
    10950 
    10951 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    10952 
    10953 > select #4/A-D,H-J
    10954 
    10955 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10956 
    10957 > select #5/D,F
    10958 
    10959 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    10960 
    10961 > select #6/G-V
    10962 
    10963 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    10964 
    10965 > select clear
    10966 
    10967 > select #4/A-D,H-J
    10968 
    10969 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10970 
    10971 > select #5/D,F
    10972 
    10973 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    10974 
    10975 > select #6/G-V
    10976 
    10977 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    10978 
    10979 > select clear
    10980 
    10981 [Repeated 1 time(s)]
    10982 
    10983 > select #4/A-D,H-J
    10984 
    10985 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    10986 
    10987 > select #5/D,F
    10988 
    10989 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    10990 
    10991 > select #6/G-V
    10992 
    10993 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    10994 
    10995 > select add #5
    10996 
    10997 29378 atoms, 29854 bonds, 66 pseudobonds, 3597 residues, 3 models selected 
    10998 
    10999 > select add #4
    11000 
    11001 57477 atoms, 58516 bonds, 114 pseudobonds, 7027 residues, 6 models selected 
    11002 
    11003 > select #4/A-D,H-J
    11004 
    11005 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    11006 
    11007 > select #5/D,F
    11008 
    11009 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    11010 
    11011 > select #6/G-V
    11012 
    11013 25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected 
    11014 
    11015 > select #4/A-D,H-J
    11016 
    11017 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    11018 
    11019 > select #5/D,F
    11020 
    11021 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    11022 
    11023 > color sel red
    11024 
    11025 > select clear
    11026 
    11027 > select #4/A-D,H-J
    11028 
    11029 11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected 
    11030 
    11031 > select clear
    11032 
    11033 > select add #6
    11034 
    11035 39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected 
    11036 
    11037 > select subtract #6
    11038 
    11039 Nothing selected 
    11040 
    11041 > hide #!6 models
    11042 
    11043 > select add #6
    11044 
    11045 39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected 
    11046 
    11047 > select subtract #6
    11048 
    11049 Nothing selected 
    11050 
    11051 > show #!6 models
    11052 
    11053 > hide #!6 models
    11054 
    11055 > show #!6 models
    11056 
    11057 > hide #!6 models
    11058 
    11059 > select #4/A-B
    11060 
    11061 3475 atoms, 3533 bonds, 7 pseudobonds, 428 residues, 2 models selected 
    11062 
    11063 > show #!6 models
    11064 
    11065 > hide #!6 models
    11066 
    11067 > show #!6 models
    11068 
    11069 > hide #!6 models
    11070 
    11071 > show #!6 models
    11072 
    11073 > hide #!6 models
    11074 
    11075 > select #4/C-D
    11076 
    11077 3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected 
    11078 Alignment identifier is 1 
    11079 
    11080 > select #4/C-D:357
    11081 
    11082 Nothing selected 
    11083 
    11084 > select clear
    11085 
    11086 [Repeated 3 time(s)]
    11087 
    11088 > select #4/C:331
    11089 
    11090 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11091 
    11092 > select #4/C:326-331/D:326-328
    11093 
    11094 73 atoms, 71 bonds, 9 residues, 1 model selected 
    11095 
    11096 > select #4/C-D:317
    11097 
    11098 16 atoms, 14 bonds, 2 residues, 1 model selected 
    11099 
    11100 > select #4/C-D:282-317
    11101 
    11102 602 atoms, 620 bonds, 72 residues, 1 model selected 
    11103 
    11104 > select #4/C:134-138,195-196,233-239,262-270,329-331/D:112
    11105 
    11106 173 atoms, 168 bonds, 1 pseudobond, 23 residues, 2 models selected 
    11107 
    11108 > select #4/C:331
    11109 
    11110 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11111 
    11112 > select #4/C:329-331
    11113 
    11114 25 atoms, 24 bonds, 3 residues, 1 model selected 
    11115 
    11116 > select #4/C-D:331
    11117 
    11118 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11119 
    11120 > select #4/C-D:331\0
    11121 
    11122 Nothing selected 
    11123 
    11124 > select #4/C-D:330
    11125 
    11126 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11127 
    11128 > select #4/C-D:325
    11129 
    11130 22 atoms, 22 bonds, 2 residues, 1 model selected 
    11131 
    11132 > select #5/D,F
    11133 
    11134 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    11135 Alignment identifier is 1 
    11136 
    11137 > select #5/D:76-77
    11138 
    11139 12 atoms, 11 bonds, 2 residues, 1 model selected 
    11140 
    11141 > select #5/D:70-77
    11142 
    11143 54 atoms, 54 bonds, 8 residues, 1 model selected 
    11144 
    11145 > select #5/D:68-69
    11146 
    11147 13 atoms, 12 bonds, 2 residues, 1 model selected 
    11148 
    11149 > select #5/D:56-69/F:56-64
    11150 
    11151 182 atoms, 180 bonds, 23 residues, 1 model selected 
    11152 
    11153 > select #5/D:71-72
    11154 
    11155 15 atoms, 14 bonds, 2 residues, 1 model selected 
    11156 
    11157 > select #5/D:71-78
    11158 
    11159 54 atoms, 54 bonds, 8 residues, 1 model selected 
    11160 
    11161 > select #4/C-D
    11162 
    11163 3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected 
    11164 
    11165 > select #4-6
    11166 
    11167 70652 atoms, 72241 bonds, 262 pseudobonds, 8461 residues, 7 models selected 
    11168 
    11169 > color (#5#!4 & sel) light gray
    11170 
    11171 > select #4/C,D
    11172 
    11173 3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected 
    11174 
    11175 > color (#!4 & sel) red
    11176 
    11177 > select #5/D,F
    11178 
    11179 1113 atoms, 1132 bonds, 139 residues, 1 model selected 
    11180 
    11181 > color sel red
    11182 
    11183 > select #5/D,F and #4/C,D
    11184 
    11185 Expected a keyword 
    11186 
    11187 > select #3
    11188 
    11189 2 models selected 
    11190 
    11191 > select clear
    11192 
    11193 > select #5/D:68
    11194 
    11195 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11196 
    11197 > select #5/D:63-68/F:63-64
    11198 
    11199 58 atoms, 56 bonds, 8 residues, 1 model selected 
    11200 
    11201 > select #5/D,F:62
    11202 
    11203 16 atoms, 14 bonds, 2 residues, 1 model selected 
    11204 
    11205 > select #5/D,F:52-62
    11206 
    11207 176 atoms, 176 bonds, 22 residues, 1 model selected 
    11208 
    11209 > select #5/D,F:63-64
    11210 
    11211 32 atoms, 30 bonds, 4 residues, 1 model selected 
    11212 
    11213 > select #5/D:63-73/F:63-64
    11214 
    11215 98 atoms, 97 bonds, 13 residues, 1 model selected 
    11216 
    11217 > select #4/C,D
    11218 
    11219 3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected 
    11220 Alignment identifier is 2 
    11221 
    11222 > select #6/I,J,M,N,Q,R,U,V
    11223 
    11224 13297 atoms, 13514 bonds, 29 pseudobonds, 1601 residues, 2 models selected 
    11225 
    11226 > show #!6 models
    11227 
    11228 Alignment identifier is 3 
    11229 
    11230 > hide #!6 models
    11231 
    11232 > hide #5 models
    11233 
    11234 > ui tool show "Fit in Map"
    11235 
    11236 > volume #2 step 1
    11237 
    11238 > volume #3 step 1
    11239 
    11240 > volume #7 step 1
    11241 
    11242 > select add #6
    11243 
    11244 39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected 
    11245 
    11246 > select subtract #6
    11247 
    11248 Nothing selected 
    11249 
    11250 > fitmap #4 inMap #3
    11251 
    11252 Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms 
    11253 average map value = 0.008828, steps = 108 
    11254 shifted from previous position = 11.2 
    11255 rotated from previous position = 1.68 degrees 
    11256 atoms outside contour = 10700, contour level = 0.0073443 
    11257  
    11258 Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates: 
    11259 Matrix rotation and translation 
    11260 0.90100599 -0.43380661 0.00018630 179.75327232 
    11261 0.43380654 0.90100598 0.00032773 -113.12278354 
    11262 -0.00031003 -0.00021447 0.99999993 0.22425752 
    11263 Axis -0.00062493 0.00057206 0.99999964 
    11264 Axis point 337.73732720 337.29160338 0.00000000 
    11265 Rotation angle (degrees) 25.70938878 
    11266 Shift along axis 0.04721037 
    11267  
    11268 
    11269 > fitmap #4 inMap #3
    11270 
    11271 Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms 
    11272 average map value = 0.008828, steps = 44 
    11273 shifted from previous position = 0.00395 
    11274 rotated from previous position = 0.00358 degrees 
    11275 atoms outside contour = 10704, contour level = 0.0073443 
    11276  
    11277 Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates: 
    11278 Matrix rotation and translation 
    11279 0.90101456 -0.43378882 0.00013329 179.75565688 
    11280 0.43378877 0.90101455 0.00030136 -113.11017006 
    11281 -0.00025082 -0.00021371 0.99999995 0.20056965 
    11282 Axis -0.00059369 0.00044274 0.99999973 
    11283 Axis point 337.72213240 337.32106882 0.00000000 
    11284 Rotation angle (degrees) 25.70825572 
    11285 Shift along axis 0.04377270 
    11286  
    11287 
    11288 > volume #2 level 0.008402
    11289 
    11290 > volume #2 level 0.008189
    11291 
    11292 > volume #3 level 0.007416
    11293 
    11294 > volume #7 level 0.008601
    11295 
    11296 > volume #7 level 0.00667
    11297 
    11298 > fitmap #2 inMap #1
    11299 
    11300 Fit map emd_51809.map in map emd_51794.map using 256025 points 
    11301 correlation = 0.9048, correlation about mean = 0.152, overlap = 17.5 
    11302 steps = 40, shift = 0.0494, angle = 0.022 degrees 
    11303  
    11304 Position of emd_51809.map (#2) relative to emd_51794.map (#1) coordinates: 
    11305 Matrix rotation and translation 
    11306 0.99757329 0.06940982 0.00545947 119.41870490 
    11307 -0.06941176 0.99758808 0.00016676 148.88130709 
    11308 -0.00543473 -0.00054531 0.99998508 236.75638760 
    11309 Axis -0.00511360 0.07823468 -0.99692186 
    11310 Axis point 2454.71468207 -1618.08965596 0.00000000 
    11311 Rotation angle (degrees) 3.99245500 
    11312 Shift along axis -224.99059556 
    11313  
    11314 
    11315 > fitmap #3 inMap #1
    11316 
    11317 Fit map emd_51808.map in map emd_51794.map using 1222611 points 
    11318 correlation = 0.9653, correlation about mean = 0.5741, overlap = 122 
    11319 steps = 28, shift = 0.00253, angle = 0.00246 degrees 
    11320  
    11321 Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates: 
    11322 Matrix rotation and translation 
    11323 0.99956421 0.02951925 0.00000072 -9.81624044 
    11324 -0.02951925 0.99956421 -0.00000024 10.10990167 
    11325 -0.00000073 0.00000022 1.00000000 -10.09814507 
    11326 Axis 0.00000768 0.00002460 -1.00000000 
    11327 Axis point 337.49379423 337.52186297 0.00000000 
    11328 Rotation angle (degrees) 1.69157444 
    11329 Shift along axis 10.09831833 
    11330  
    11331 
    11332 > fitmap #3 inMap #1
    11333 
    11334 Fit map emd_51808.map in map emd_51794.map using 1222611 points 
    11335 correlation = 0.9653, correlation about mean = 0.5741, overlap = 122 
    11336 steps = 40, shift = 0.03, angle = 0.000315 degrees 
    11337  
    11338 Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates: 
    11339 Matrix rotation and translation 
    11340 0.99956405 0.02952465 -0.00000031 -9.81701875 
    11341 -0.02952465 0.99956405 0.00000009 10.11164600 
    11342 0.00000032 -0.00000008 1.00000000 -10.06841949 
    11343 Axis -0.00000278 -0.00001066 -1.00000000 
    11344 Axis point 337.50199711 337.48493379 0.00000000 
    11345 Rotation angle (degrees) 1.69188359 
    11346 Shift along axis 10.06833899 
    11347  
    11348 
    11349 > fitmap #7 inMap #1
    11350 
    11351 Fit map emd_51803.map in map emd_51794.map using 343453 points 
    11352 correlation = 0.81, correlation about mean = 0.01007, overlap = 15.6 
    11353 steps = 40, shift = 0.0562, angle = 0.22 degrees 
    11354  
    11355 Position of emd_51803.map (#7) relative to emd_51794.map (#1) coordinates: 
    11356 Matrix rotation and translation 
    11357 0.68982040 -0.72398053 -0.00001049 344.42004511 
    11358 0.72398053 0.68982040 -0.00000583 51.20703324 
    11359 0.00001146 -0.00000357 1.00000000 123.90862912 
    11360 Axis 0.00000156 -0.00001516 1.00000000 
    11361 Axis point 112.44736376 427.55427785 0.00000000 
    11362 Rotation angle (degrees) 46.38410619 
    11363 Shift along axis 123.90838894 
    11364  
    11365 
    11366 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    11367 
    11368 > graphics silhouettes true
    11369 
    11370 > lighting depthCue false
    11371 
    11372 > lighting soft
    11373 
    11374 > graphics bgColor white
    11375 
    11376 > graphics silhouettes width 2.3
    11377 
    11378 > cartoon style protein modeHelix tube radius 1.9 sides 24
    11379 
    11380 > graphics silhouettes width 2
    11381 
    11382 > cartoon style protein modeHelix tube radius 1.9 sides 24
    11383 
    11384 > select #2,3,4,7
    11385 
    11386 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 9 models selected 
    11387 
    11388 > color (#!4 & sel) #8c8dfcff
    11389 
    11390 > select #2,3,7
    11391 
    11392 6 models selected 
    11393 
    11394 > select clear
    11395 
    11396 > color #7 #8c8dfcff models
    11397 
    11398 > color #3 #8c8dfcff models
    11399 
    11400 > color #2 #8c8dfcff models
    11401 
    11402 > transparency #2,3,7 70
    11403 
    11404 > color #4 #c1153cff
    11405 
    11406 > $4 info
    11407 
    11408 Unknown command: $4 info 
    11409 
    11410 > ui tool show "Hide Dust"
    11411 
    11412 > surface dust #2 size 8.1
    11413 
    11414 > surface dust #2 size 7.62
    11415 
    11416 > surface dust #2 size 6.78
    11417 
    11418 > surface dust #3 size 8.1
    11419 
    11420 > surface dust #7 size 8.1
    11421 
    11422 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    11423 
    11424 ——— End of log from Mon Jun 9 21:58:32 2025 ———
    11425 
    11426 opened ChimeraX session 
    11427 
    11428 > open .8I8B
    11429 
    11430 '.8I8B' has no suffix 
    11431 
    11432 > open 8I8B
    11433 
    11434 Summary of feedback from opening 8I8B fetched from pdb 
    11435 --- 
    11436 note | Fetching compressed mmCIF 8i8b from http://files.rcsb.org/download/8i8b.cif 
    11437  
    11438 8i8b title: 
    11439 Outer shell and inner layer structures of Autographa californica multiple
    11440 nucleopolyhedrovirus (AcMNPV) [more info...] 
    11441  
    11442 Chain information for 8i8b #8 
    11443 --- 
    11444 Chain | Description | UniProt 
    11445 A B C | Viral capsid associated protein | A0A0N7CTI8_9ABAC 1-691 
    11446 D | AcOrf-109 peptide | A0A0N7CRZ7_9ABAC 1-390 
    11447 E | Early 49 Daa protein | A0A0N7CTL8_9ABAC 1-477 
    11448 F G | P40 | A0A0N7CQX9_9ABAC 1-361 
    11449 H I | Occlusion-derived virus envelope/capsid protein | A0A0N7CT36_9ABAC 1-290 
    11450 J | 38K | A0A0N7CSX4_9ABAC 1-320 
    11451 W X Y Z | Major viral capsid protein | A0A0N6WHR0_9ABAC 1-347 
    11452  
    11453 
    11454 > select add #8
    11455 
    11456 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    11457 
    11458 > hide sel atoms
    11459 
    11460 > show sel cartoons
    11461 
    11462 > view matrix models #8,1,0,0,-194.13,0,1,0,228.1,0,0,1,8.5426
    11463 
    11464 > select #8/A-C
    11465 
    11466 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    11467 
    11468 > view matrix models #8,1,0,0,-166.55,0,1,0,261.45,0,0,1,-9.8791
    11469 
    11470 > ui mousemode right "rotate selected models"
    11471 
    11472 > view matrix models
    11473 > #8,-0.29376,0.95472,-0.047067,151.85,-0.097249,0.019134,0.99508,200.81,0.95092,0.29689,0.087225,-163.66
    11474 
    11475 > view matrix models
    11476 > #8,-0.79614,-0.30724,-0.52131,839.07,0.23184,-0.95065,0.20621,577.91,-0.55894,0.043311,0.82808,271.91
    11477 
    11478 > view matrix models
    11479 > #8,-0.67014,0.36916,-0.64392,661.02,-0.21272,-0.92667,-0.30988,936.1,-0.7111,-0.070687,0.69953,408.2
    11480 
    11481 > view matrix models
    11482 > #8,-0.74305,0.17658,-0.64551,739.8,-0.10392,-0.98331,-0.14936,849.19,-0.66111,-0.0439,0.749,363.56
    11483 
    11484 > view matrix models
    11485 > #8,-0.78629,0.33233,-0.52086,675.94,-0.28602,-0.94304,-0.16992,922.21,-0.54766,0.015373,0.83656,271.21
    11486 
    11487 > ui mousemode right "translate selected models"
    11488 
    11489 > view matrix models
    11490 > #8,-0.78629,0.33233,-0.52086,772.67,-0.28602,-0.94304,-0.16992,937.74,-0.54766,0.015373,0.83656,315.23
    11491 
    11492 > view matrix models
    11493 > #8,-0.78629,0.33233,-0.52086,773.25,-0.28602,-0.94304,-0.16992,901.12,-0.54766,0.015373,0.83656,309.88
    11494 
    11495 > view matrix models
    11496 > #8,-0.78629,0.33233,-0.52086,777.17,-0.28602,-0.94304,-0.16992,914.61,-0.54766,0.015373,0.83656,282.01
    11497 
    11498 > view matrix models
    11499 > #8,-0.78629,0.33233,-0.52086,784.37,-0.28602,-0.94304,-0.16992,914.8,-0.54766,0.015373,0.83656,278.95
    11500 
    11501 > ui mousemode right "rotate selected models"
    11502 
    11503 > view matrix models
    11504 > #8,-0.87051,-0.081637,-0.48532,909.99,-0.017541,-0.98037,0.19637,685.23,-0.49183,0.17946,0.852,209.56
    11505 
    11506 > view matrix models
    11507 > #8,-0.62906,-0.70166,-0.3346,911.14,0.67477,-0.70659,0.21313,322.86,-0.38597,-0.091701,0.91794,209.94
    11508 
    11509 > view matrix models
    11510 > #8,-0.60815,-0.79075,-0.069816,832.79,0.75341,-0.54725,-0.36454,450.69,0.25006,-0.2743,0.92857,-13.478
    11511 
    11512 > ui mousemode right "translate selected models"
    11513 
    11514 > view matrix models
    11515 > #8,-0.60815,-0.79075,-0.069816,812.29,0.75341,-0.54725,-0.36454,456.13,0.25006,-0.2743,0.92857,-31.86
    11516 
    11517 > view matrix models
    11518 > #8,-0.60815,-0.79075,-0.069816,809.39,0.75341,-0.54725,-0.36454,463.01,0.25006,-0.2743,0.92857,-30.773
    11519 
    11520 > ui mousemode right "rotate selected models"
    11521 
    11522 > view matrix models
    11523 > #8,-0.63427,-0.77305,0.0094979,788.4,0.72714,-0.60068,-0.33233,476.07,0.26262,-0.20388,0.94311,-58.543
    11524 
    11525 > view matrix models
    11526 > #8,-0.81433,-0.56112,-0.14834,865.5,0.57604,-0.7501,-0.32485,573.58,0.07101,-0.34998,0.93406,60.75
    11527 
    11528 > ui tool show "Fit in Map"
    11529 
    11530 > fitmap #8 inMap #3
    11531 
    11532 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11533 average map value = 0.007156, steps = 296 
    11534 shifted from previous position = 27.1 
    11535 rotated from previous position = 31.1 degrees 
    11536 atoms outside contour = 16477, contour level = 0.0074163 
    11537  
    11538 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11539 Matrix rotation and translation 
    11540 -0.99159287 -0.12939173 -0.00118038 791.13260992 
    11541 0.12900294 -0.98781957 -0.08701022 715.09802323 
    11542 0.01009240 -0.08643099 0.99620674 15.43363463 
    11543 Axis 0.00223950 -0.04358465 0.99904723 
    11544 Axis point 372.32996800 383.59644668 0.00000000 
    11545 Rotation angle (degrees) 172.56966900 
    11546 Shift along axis -13.97662982 
    11547  
    11548 
    11549 > hide #!4 models
    11550 
    11551 > show #!4 models
    11552 
    11553 > hide #!4 models
    11554 
    11555 Alignment identifier is 1 
    11556 
    11557 > select ~sel & ##selected
    11558 
    11559 24966 atoms, 25528 bonds, 8 pseudobonds, 3055 residues, 2 models selected 
    11560 
    11561 > hide sel cartoons
    11562 
    11563 > show #!4 models
    11564 
    11565 > select #8H-J
    11566 
    11567 Expected an objects specifier or a keyword 
    11568 
    11569 > select #4/H-J
    11570 
    11571 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    11572 
    11573 > select down
    11574 
    11575 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    11576 
    11577 > select ~sel & ##selected
    11578 
    11579 23413 atoms, 23880 bonds, 44 pseudobonds, 2869 residues, 3 models selected 
    11580 
    11581 > hide sel cartoons
    11582 
    11583 > select clear
    11584 
    11585 Alignment identifier is 2 
    11586 Alignment identifier is 3 
    11587 Alignment identifier is 4 
    11588 Alignment identifier is 5 
    11589 Alignment identifier is 6 
    11590 Alignment identifier is 7 
    11591 Alignment identifier is 8 
    11592 Alignment identifier is 4/O 
    11593 Alignment identifier is 9 
    11594 Alignment identifier is 10 
    11595 Alignment identifier is 6/E 
    11596 Alignment identifier is 6/F 
    11597 Alignment identifier is 8/J 
    11598 
    11599 > select #4/H-J
    11600 
    11601 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    11602 Alignment identifier is 1 
    11603 
    11604 > select #8/A-C
    11605 
    11606 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    11607 Alignment identifier is 2 
    11608 
    11609 > select clear
    11610 
    11611 > select #4/H-J:536
    11612 
    11613 24 atoms, 21 bonds, 3 residues, 1 model selected 
    11614 
    11615 > select #4/H-J:536-544
    11616 
    11617 237 atoms, 240 bonds, 27 residues, 1 model selected 
    11618 
    11619 > hide #!4 models
    11620 
    11621 > show #!4 models
    11622 
    11623 > select #8/A-C:674
    11624 
    11625 21 atoms, 18 bonds, 3 residues, 1 model selected 
    11626 
    11627 > select #8/A-C:674-680
    11628 
    11629 186 atoms, 186 bonds, 21 residues, 1 model selected 
    11630 
    11631 > select #4/H:674
    11632 
    11633 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11634 
    11635 > select #4/H:674-682
    11636 
    11637 78 atoms, 78 bonds, 9 residues, 1 model selected 
    11638 
    11639 > graphics silhouettes width 2
    11640 
    11641 > cartoon style protein modeHelix tube radius 1.9 sides 24
    11642 
    11643 > graphics silhouettes true
    11644 
    11645 > lighting depthCue false
    11646 
    11647 > lighting soft
    11648 
    11649 > graphics bgColor white
    11650 
    11651 > select clear
    11652 
    11653 > hide #!4 models
    11654 
    11655 > show #!4 models
    11656 
    11657 > select #4/H:674
    11658 
    11659 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11660 
    11661 > select #4/H:674-685
    11662 
    11663 102 atoms, 102 bonds, 12 residues, 1 model selected 
    11664 
    11665 > select #4/H-J:652
    11666 
    11667 24 atoms, 21 bonds, 3 residues, 1 model selected 
    11668 
    11669 > select #4/H:652-663/I:652-662/J:652-666
    11670 
    11671 312 atoms, 316 bonds, 38 residues, 1 model selected 
    11672 
    11673 > select clear
    11674 
    11675 > hide #!4 models
    11676 
    11677 > color #8 #c1153cff
    11678 
    11679 > select clear
    11680 
    11681 > show #!4 models
    11682 
    11683 > hide #!8 models
    11684 
    11685 > show #!8 models
    11686 
    11687 > hide #!8 models
    11688 
    11689 > show #!8 models
    11690 
    11691 > hide #!8 models
    11692 
    11693 > show #!8 models
    11694 
    11695 > hide #!8 models
    11696 
    11697 > show #!8 models
    11698 
    11699 > hide #!8 models
    11700 
    11701 > show #!8 models
    11702 
    11703 > hide #!4 models
    11704 
    11705 > fitmap #8 inMap #3
    11706 
    11707 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11708 average map value = 0.007155, steps = 84 
    11709 shifted from previous position = 0.0221 
    11710 rotated from previous position = 0.0113 degrees 
    11711 atoms outside contour = 16466, contour level = 0.0074163 
    11712  
    11713 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11714 Matrix rotation and translation 
    11715 -0.99158624 -0.12944071 -0.00136543 791.20111863 
    11716 0.12906819 -0.98781514 -0.08696368 715.04336589 
    11717 0.00990785 -0.08640823 0.99621057 15.52431854 
    11718 Axis 0.00214663 -0.04356736 0.99904819 
    11719 Axis point 372.35625880 383.58455770 0.00000000 
    11720 Rotation angle (degrees) 172.56637270 
    11721 Shift along axis -13.94459507 
    11722  
    11723 
    11724 > fitmap #8 inMap #3
    11725 
    11726 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11727 average map value = 0.007156, steps = 100 
    11728 shifted from previous position = 0.0204 
    11729 rotated from previous position = 0.00235 degrees 
    11730 atoms outside contour = 16464, contour level = 0.0074163 
    11731  
    11732 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11733 Matrix rotation and translation 
    11734 -0.99158733 -0.12943270 -0.00133408 791.19962794 
    11735 0.12905776 -0.98781871 -0.08693861 715.05186086 
    11736 0.00993487 -0.08637941 0.99621280 15.49199880 
    11737 Axis 0.00216129 -0.04355377 0.99904875 
    11738 Axis point 372.35686539 383.58607426 0.00000000 
    11739 Rotation angle (degrees) 172.56691018 
    11740 Shift along axis -13.95592675 
    11741  
    11742 
    11743 > fitmap #8 inMap #3
    11744 
    11745 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11746 average map value = 0.007155, steps = 64 
    11747 shifted from previous position = 0.0187 
    11748 rotated from previous position = 0.00323 degrees 
    11749 atoms outside contour = 16465, contour level = 0.0074163 
    11750  
    11751 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11752 Matrix rotation and translation 
    11753 -0.99158276 -0.12946725 -0.00137838 791.21789539 
    11754 0.12909601 -0.98781379 -0.08693780 715.02106183 
    11755 0.00989402 -0.08638398 0.99621281 15.52329661 
    11756 Axis 0.00213990 -0.04355482 0.99904875 
    11757 Axis point 372.36051482 383.57925493 0.00000000 
    11758 Rotation angle (degrees) 172.56480470 
    11759 Shift along axis -13.94095442 
    11760  
    11761 
    11762 > fitmap #8 inMap #3
    11763 
    11764 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11765 average map value = 0.007156, steps = 64 
    11766 shifted from previous position = 0.0224 
    11767 rotated from previous position = 0.00913 degrees 
    11768 atoms outside contour = 16469, contour level = 0.0074163 
    11769  
    11770 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11771 Matrix rotation and translation 
    11772 -0.99156918 -0.12957220 -0.00127860 791.20518211 
    11773 0.12919260 -0.98780689 -0.08687266 714.97140200 
    11774 0.00999328 -0.08630545 0.99621862 15.44343915 
    11775 Axis 0.00218993 -0.04351894 0.99905020 
    11776 Axis point 372.33728097 383.57216645 0.00000000 
    11777 Rotation angle (degrees) 172.55898753 
    11778 Shift along axis -13.95334073 
    11779  
    11780 
    11781 > fitmap #8 inMap #3
    11782 
    11783 Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms 
    11784 average map value = 0.007156, steps = 96 
    11785 shifted from previous position = 0.0141 
    11786 rotated from previous position = 0.0167 degrees 
    11787 atoms outside contour = 16467, contour level = 0.0074163 
    11788  
    11789 Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates: 
    11790 Matrix rotation and translation 
    11791 -0.99159042 -0.12940914 -0.00131942 791.18165481 
    11792 0.12903132 -0.98780716 -0.08710897 715.12188799 
    11793 0.00996936 -0.08654668 0.99619793 15.53024467 
    11794 Axis 0.00217365 -0.04363871 0.99904501 
    11795 Axis point 372.34988316 383.61718039 0.00000000 
    11796 Rotation angle (degrees) 172.56832828 
    11797 Shift along axis -13.97182858 
    11798  
    11799 
    11800 > transparency #2,3,7 60
    11801 
    11802 > transparency #2,3,7 68
    11803 
    11804 > color #7 #d2d2d3ff models
    11805 
    11806 > color #7 #d2d2d399 models
    11807 
    11808 > color #7 #d2d2d3f4 models
    11809 
    11810 > color #7 #d2d2d3b3 models
    11811 
    11812 > hide #!3 models
    11813 
    11814 > color #3 #d2d2d3ff models
    11815 
    11816 > color #3 #d2d2d3b2 models
    11817 
    11818 > show #!3 models
    11819 
    11820 > hide #!2 models
    11821 
    11822 > show #!2 models
    11823 
    11824 > color #2 #d2d2d3ff models
    11825 
    11826 > color #2 #d2d2d3b2 models
    11827 
    11828 > ligghting soft\
    11829 
    11830 Unknown command: ligghting soft\ 
    11831 
    11832 > ligghting soft
    11833 
    11834 Unknown command: ligghting soft 
    11835 
    11836 > lioghting soft
    11837 
    11838 Unknown command: lioghting soft 
    11839 
    11840 > lighting soft
    11841 
    11842 > lighting gentle
    11843 
    11844 > lighting soft
    11845 
    11846 > lighting gentle
    11847 
    11848 > transparency #2,3,7 75
    11849 
    11850 > transparency #2,3,7 70
    11851 
    11852 > transparency #2,3,7 65
    11853 
    11854 > lighting soft
    11855 
    11856 > lighting gentle
    11857 
    11858 > lighting soft
    11859 
    11860 > lighting gentle
    11861 
    11862 > lighting soft
    11863 
    11864 > transparency #2,3,7 60
    11865 
    11866 > color #7 #c2cafdff models
    11867 
    11868 > color #3 #c2cafdff models
    11869 
    11870 > color #2 #c2cafdff models
    11871 
    11872 > transparency #2,3,7 60
    11873 
    11874 > select #8/A:534
    11875 
    11876 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11877 
    11878 > select up
    11879 
    11880 74 atoms, 74 bonds, 9 residues, 1 model selected 
    11881 
    11882 > select up
    11883 
    11884 1455 atoms, 1487 bonds, 175 residues, 1 model selected 
    11885 
    11886 > color sel #c1153cff
    11887 
    11888 > color sel #be3c51ff
    11889 
    11890 > color sel #be3b51ff
    11891 
    11892 > color sel #bb3b50ff
    11893 
    11894 > color sel #b7394eff
    11895 
    11896 > color sel #b4384dff
    11897 
    11898 > color sel #b2384cff
    11899 
    11900 > color sel #b1384cff
    11901 
    11902 > color sel #b1374bff
    11903 
    11904 > color sel #b0374bff
    11905 
    11906 > color sel #ae374aff
    11907 
    11908 > color sel #ad364aff
    11909 
    11910 > color sel #a83548ff
    11911 
    11912 > color sel #a63447ff
    11913 
    11914 > color sel #a23345ff
    11915 
    11916 > color sel #9e3143ff
    11917 
    11918 > color sel #9a3042ff
    11919 
    11920 > color sel #962f40ff
    11921 
    11922 > color sel #912d3eff
    11923 
    11924 > color sel #8e2c3cff
    11925 
    11926 > color sel #8d2c3cff
    11927 
    11928 [Repeated 1 time(s)]
    11929 
    11930 > color sel #8c2c3cff
    11931 
    11932 > color sel #8a2b3bff
    11933 
    11934 > color sel #882a3aff
    11935 
    11936 > color sel #832938ff
    11937 
    11938 > color sel #802836ff
    11939 
    11940 > color sel #792633ff
    11941 
    11942 > color sel #782633ff
    11943 
    11944 [Repeated 1 time(s)]
    11945 
    11946 > color sel #762532ff
    11947 
    11948 > color sel #722431ff
    11949 
    11950 > color sel #722430ff
    11951 
    11952 > color sel #722431ff
    11953 
    11954 > color sel #742431ff
    11955 
    11956 > color sel #762532ff
    11957 
    11958 > color sel #782633ff
    11959 
    11960 > color sel #7a2634ff
    11961 
    11962 > color sel #7b2634ff
    11963 
    11964 > color sel #7b2735ff
    11965 
    11966 > color sel #7c2735ff
    11967 
    11968 > color sel #7d2735ff
    11969 
    11970 [Repeated 1 time(s)]
    11971 
    11972 > color sel #7e2736ff
    11973 
    11974 > color sel #802836ff
    11975 
    11976 > color sel #862a39ff
    11977 
    11978 > color sel #8b2c3bff
    11979 
    11980 > color sel #8e2c3cff
    11981 
    11982 > color sel #902d3dff
    11983 
    11984 > color sel #912d3eff
    11985 
    11986 > color sel #912e3eff
    11987 
    11988 > color sel #922e3eff
    11989 
    11990 [Repeated 1 time(s)]
    11991 
    11992 > color sel #932e3fff
    11993 
    11994 [Repeated 2 time(s)]
    11995 
    11996 > color sel #942e3fff
    11997 
    11998 > color sel #932e3fff
    11999 
    12000 > color sel #922e3eff
    12001 
    12002 > color sel #912d3eff
    12003 
    12004 > color sel #902d3eff
    12005 
    12006 > color sel #8e2c3cff
    12007 
    12008 > color sel #8c2c3cff
    12009 
    12010 > color sel #8b2c3bff
    12011 
    12012 [Repeated 1 time(s)]
    12013 
    12014 > color sel #892b3aff
    12015 
    12016 > color sel #872a3aff
    12017 
    12018 > color sel #852a39ff
    12019 
    12020 [Repeated 1 time(s)]
    12021 
    12022 > color sel #842938ff
    12023 
    12024 [Repeated 1 time(s)]
    12025 
    12026 > color sel #832938ff
    12027 
    12028 > color sel #802837ff
    12029 
    12030 > color sel #802836ff
    12031 
    12032 > color sel #792634ff
    12033 
    12034 > color sel #772533ff
    12035 
    12036 > color sel #752532ff
    12037 
    12038 > color sel #742432ff
    12039 
    12040 > color sel #752532ff
    12041 
    12042 [Repeated 1 time(s)]
    12043 
    12044 > color sel #762532ff
    12045 
    12046 [Repeated 1 time(s)]
    12047 
    12048 > color sel #772533ff
    12049 
    12050 > color sel #762532ff
    12051 
    12052 > color sel #752532ff
    12053 
    12054 > color sel #722431ff
    12055 
    12056 [Repeated 1 time(s)]
    12057 
    12058 > color sel #732431ff
    12059 
    12060 > color sel #742431ff
    12061 
    12062 > select up
    12063 
    12064 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    12065 
    12066 > select down
    12067 
    12068 1455 atoms, 1487 bonds, 175 residues, 1 model selected 
    12069 
    12070 > select up
    12071 
    12072 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    12073 
    12074 > select up
    12075 
    12076 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    12077 
    12078 > select down
    12079 
    12080 1463 atoms, 1494 bonds, 176 residues, 1 model selected 
    12081 
    12082 > select up
    12083 
    12084 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    12085 
    12086 > select up
    12087 
    12088 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    12089 
    12090 > select down
    12091 
    12092 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    12093 
    12094 > select up
    12095 
    12096 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    12097 
    12098 > select down
    12099 
    12100 1565 atoms, 1597 bonds, 188 residues, 1 model selected 
    12101 
    12102 > select up
    12103 
    12104 30015 atoms, 30679 bonds, 3660 residues, 1 model selected 
    12105 
    12106 > select clear
    12107 
    12108 > select add #8
    12109 
    12110 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    12111 
    12112 > select subtract #8
    12113 
    12114 Nothing selected 
    12115 
    12116 > select add #8
    12117 
    12118 30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected 
    12119 
    12120 > color #8 #bb3b50ff
    12121 
    12122 > color #8 #c1153cff
    12123 
    12124 > color #8 #bb3b50ff
    12125 
    12126 [Repeated 1 time(s)]
    12127 
    12128 > select #8/A
    12129 
    12130 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    12131 
    12132 > color (#!8 & sel) #bb3c53ff
    12133 
    12134 > color (#!8 & sel) #ba3c53ff
    12135 
    12136 > color (#!8 & sel) #b43a50ff
    12137 
    12138 > color (#!8 & sel) #b1394fff
    12139 
    12140 > color (#!8 & sel) #b0384eff
    12141 
    12142 > color (#!8 & sel) #a8364bff
    12143 
    12144 > color (#!8 & sel) #942f42ff
    12145 
    12146 > color (#!8 & sel) #8e2e3fff
    12147 
    12148 > color (#!8 & sel) #8b2d3dff
    12149 
    12150 > color (#!8 & sel) #852b3bff
    12151 
    12152 > color (#!8 & sel) #7e2938ff
    12153 
    12154 > color (#!8 & sel) #7e2838ff
    12155 
    12156 > color (#!8 & sel) #7d2837ff
    12157 
    12158 > color (#!8 & sel) #782735ff
    12159 
    12160 > color (#!8 & sel) #722533ff
    12161 
    12162 > color (#!8 & sel) #6e2331ff
    12163 
    12164 > color (#!8 & sel) #6a222fff
    12165 
    12166 > color (#!8 & sel) #69222eff
    12167 
    12168 > color (#!8 & sel) #68212eff
    12169 
    12170 > color (#!8 & sel) #65212dff
    12171 
    12172 > color (#!8 & sel) #63202cff
    12173 
    12174 > color (#!8 & sel) #62202cff
    12175 
    12176 > color (#!8 & sel) #611f2bff
    12177 
    12178 > color (#!8 & sel) #601f2bff
    12179 
    12180 > color (#!8 & sel) #601f2aff
    12181 
    12182 > color (#!8 & sel) #5f1f2aff
    12183 
    12184 [Repeated 1 time(s)]
    12185 
    12186 > color (#!8 & sel) #63202cff
    12187 
    12188 > color (#!8 & sel) #65202dff
    12189 
    12190 > color (#!8 & sel) #66212dff
    12191 
    12192 > color (#!8 & sel) #67212eff
    12193 
    12194 [Repeated 1 time(s)]
    12195 
    12196 > color (#!8 & sel) #621f2bff
    12197 
    12198 > color (#!8 & sel) #611f2bff
    12199 
    12200 > color (#!8 & sel) #601f2bff
    12201 
    12202 > color (#!8 & sel) #5e1e2aff
    12203 
    12204 > color (#!8 & sel) #5d1e29ff
    12205 
    12206 [Repeated 1 time(s)]
    12207 
    12208 > color (#!8 & sel) #5e1e2aff
    12209 
    12210 [Repeated 1 time(s)]
    12211 
    12212 > color (#!8 & sel) #601f2bff
    12213 
    12214 [Repeated 1 time(s)]
    12215 
    12216 > color (#!8 & sel) #611f2bff
    12217 
    12218 [Repeated 1 time(s)]
    12219 
    12220 > color (#!8 & sel) #621f2bff
    12221 
    12222 > color (#!8 & sel) #62202cff
    12223 
    12224 > color (#!8 & sel) #63202cff
    12225 
    12226 > color (#!8 & sel) #64202cff
    12227 
    12228 > color (#!8 & sel) #67212eff
    12229 
    12230 [Repeated 1 time(s)]
    12231 
    12232 > color (#!8 & sel) #62202cff
    12233 
    12234 > color (#!8 & sel) #601f2bff
    12235 
    12236 [Repeated 1 time(s)]
    12237 
    12238 > color (#!8 & sel) #611f2bff
    12239 
    12240 > color (#!8 & sel) #63202cff
    12241 
    12242 > show #!4 models
    12243 
    12244 Alignment identifier is 8/A 
    12245 
    12246 > select clear
    12247 
    12248 > select add #4
    12249 
    12250 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    12251 
    12252 > interfaces select & ~solvent
    12253 
    12254 Missing or invalid "atoms" argument: invalid atoms specifier 
    12255 Alignment identifier is 1 
    12256 Alignment identifier is 3 
    12257 Alignment identifier is 4/E 
    12258 Alignment identifier is 4 
    12259 Alignment identifier is 5 
    12260 Alignment identifier is 4/K 
    12261 Alignment identifier is 6 
    12262 Alignment identifier is 4/O 
    12263 
    12264 > select clear
    12265 
    12266 > select add #4
    12267 
    12268 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    12269 
    12270 > hide #!8 models
    12271 
    12272 > select #4/H-J
    12273 
    12274 4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected 
    12275 Alignment identifier is 1 
    12276 
    12277 > select #4/J:665
    12278 
    12279 11 atoms, 11 bonds, 1 residue, 1 model selected 
    12280 
    12281 > select #4/H:673-690/J:665-668
    12282 
    12283 185 atoms, 186 bonds, 22 residues, 1 model selected 
    12284 
    12285 > show #!8 models
    12286 
    12287 > select add #8
    12288 
    12289 30200 atoms, 30865 bonds, 10 pseudobonds, 3682 residues, 3 models selected 
    12290 Alignment identifier is 2 
    12291 Alignment identifier is 3 
    12292 Alignment identifier is 8/D 
    12293 Alignment identifier is 8/E 
    12294 Alignment identifier is 4 
    12295 Alignment identifier is 5 
    12296 Alignment identifier is 8/J 
    12297 
    12298 > select #4/H:466
    12299 
    12300 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12301 
    12302 > select #4/H:466-474
    12303 
    12304 81 atoms, 80 bonds, 9 residues, 1 model selected 
    12305 
    12306 > select #4/H:465-466
    12307 
    12308 18 atoms, 17 bonds, 2 residues, 1 model selected 
    12309 
    12310 > select #4/H:465-482
    12311 
    12312 160 atoms, 160 bonds, 18 residues, 1 model selected 
    12313 
    12314 > select #4/H:483-484
    12315 
    12316 13 atoms, 12 bonds, 2 residues, 1 model selected 
    12317 
    12318 > select #4/H:483-539/I:487-539/J:490-539
    12319 
    12320 1244 atoms, 1256 bonds, 1 pseudobond, 155 residues, 2 models selected 
    12321 
    12322 > select
    12323 > #4/H:465-510,523-542,547-557,559-600,605-632,639-663,674-685/I:487-510,523-542,547-557,559-563,565-600,605-632,639-662/J:490-510,523-542,547-557,559-600,605-632,639-666
    12324 
    12325 3977 atoms, 4034 bonds, 2 pseudobonds, 473 residues, 2 models selected 
    12326 
    12327 > select clear
    12328 
    12329 > select
    12330 > #4/H:462-489,517-521,663-690/I:487-489,517-521,561-566/J:561-566,663-668
    12331 
    12332 624 atoms, 620 bonds, 2 pseudobonds, 75 residues, 2 models selected 
    12333 
    12334 > select clear
    12335 
    12336 [Repeated 1 time(s)]
    12337 
    12338 > select #4/H:465-466
    12339 
    12340 18 atoms, 17 bonds, 2 residues, 1 model selected 
    12341 
    12342 > select #4/H:465-478
    12343 
    12344 126 atoms, 126 bonds, 14 residues, 1 model selected 
    12345 
    12346 > hide #!8 models
    12347 
    12348 > select #4/H:479
    12349 
    12350 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12351 
    12352 > select #4/H:479-489/I:487-489
    12353 
    12354 113 atoms, 112 bonds, 14 residues, 1 model selected 
    12355 
    12356 > show #!8 models
    12357 
    12358 > hide #!8 models
    12359 
    12360 > select #4/H-J:490
    12361 
    12362 24 atoms, 21 bonds, 3 residues, 1 model selected 
    12363 
    12364 > select #4/H-J:490-495
    12365 
    12366 147 atoms, 144 bonds, 18 residues, 1 model selected 
    12367 
    12368 > show #!8 models
    12369 
    12370 > hide #!4 models
    12371 
    12372 > select #4/H:464-465 #8/C:464-465
    12373 
    12374 42 atoms, 42 bonds, 4 residues, 2 models selected 
    12375 
    12376 > select #4/H:464-479 #8/C:464-479
    12377 
    12378 292 atoms, 294 bonds, 32 residues, 2 models selected 
    12379 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [464-479] RMSD:
    12380 4.944 
    12381  
    12382 
    12383 > select #4/H:481 #8/C:481
    12384 
    12385 16 atoms, 14 bonds, 2 residues, 2 models selected 
    12386 
    12387 > select #4/H:481-492/J:490-492 #8/A-B:490-492/C:481-492
    12388 
    12389 261 atoms, 258 bonds, 33 residues, 2 models selected 
    12390 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [481-492] RMSD:
    12391 3.768 
    12392  
    12393 
    12394 > select #4/H,J:493 #8/A-C:493
    12395 
    12396 45 atoms, 40 bonds, 5 residues, 2 models selected 
    12397 
    12398 > select #4/H,J:493-501 #8/A-C:493-501
    12399 
    12400 370 atoms, 365 bonds, 45 residues, 2 models selected 
    12401 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [493-501] RMSD:
    12402 1.232 
    12403  
    12404 
    12405 > show #!4 models
    12406 
    12407 > hide #!4 models
    12408 
    12409 > show #!4 models
    12410 
    12411 > hide #!4 models
    12412 
    12413 > show #!4 models
    12414 
    12415 > hide #!4 models
    12416 
    12417 > show #!4 models
    12418 
    12419 > hide #!8 models
    12420 
    12421 > show #!8 models
    12422 
    12423 > hide #!4 models
    12424 
    12425 > select clear
    12426 
    12427 > show #!4 models
    12428 
    12429 > hide #!8 models
    12430 
    12431 > show #!8 models
    12432 
    12433 > hide #!4 models
    12434 
    12435 > show #!4 models
    12436 
    12437 > hide #!8 models
    12438 
    12439 > show #!8 models
    12440 
    12441 > hide #!4 models
    12442 
    12443 > show #!4 models
    12444 
    12445 > hide #!8 models
    12446 
    12447 > select #4/H:685
    12448 
    12449 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12450 
    12451 > select #4/H:677-685
    12452 
    12453 76 atoms, 75 bonds, 9 residues, 1 model selected 
    12454 
    12455 > select #4/J:666
    12456 
    12457 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12458 
    12459 > select #4/H:659-663/I:659-662/J:659-666
    12460 
    12461 150 atoms, 151 bonds, 17 residues, 1 model selected 
    12462 
    12463 > show #!8 models
    12464 
    12465 > hide #!4 models
    12466 
    12467 > select #4/J:666 #8/C:666
    12468 
    12469 12 atoms, 10 bonds, 2 residues, 2 models selected 
    12470 
    12471 > select #4/H:659-663/J:659-666 #8/A-B:659-664/C:659-666
    12472 
    12473 287 atoms, 289 bonds, 33 residues, 2 models selected 
    12474 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [659-666] RMSD:
    12475 2.540 
    12476  
    12477 
    12478 > select #4/H:674 #8/A-C:674
    12479 
    12480 28 atoms, 24 bonds, 4 residues, 2 models selected 
    12481 
    12482 > select #4/H:674-680 #8/A-C:674-680
    12483 
    12484 248 atoms, 248 bonds, 28 residues, 2 models selected 
    12485 Capsid-associated Protein VP80 [ID: 2] region chains A,B,C,H,J [674-680] RMSD:
    12486 2.050 
    12487  
    12488 
    12489 > show #!4 models
    12490 
    12491 > hide #!8 models
    12492 
    12493 > select #4/H:674
    12494 
    12495 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12496 
    12497 > select #4/H:674-680
    12498 
    12499 62 atoms, 62 bonds, 7 residues, 1 model selected 
    12500 
    12501 > show #!8 models
    12502 
    12503 > hide #!4 models
    12504 
    12505 > select add #4
    12506 
    12507 28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected 
    12508 
    12509 > select subtract #4
    12510 
    12511 Nothing selected 
    12512 
    12513 > select #8/B
    12514 
    12515 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    12516 
    12517 > color (#!8 & sel) #63202cff
    12518 
    12519 > color (#!8 & sel) #65202dff
    12520 
    12521 > color (#!8 & sel) #66212dff
    12522 
    12523 > color (#!8 & sel) #68212eff
    12524 
    12525 > color (#!8 & sel) #69222eff
    12526 
    12527 > color (#!8 & sel) #69222fff
    12528 
    12529 [Repeated 1 time(s)]
    12530 
    12531 > color (#!8 & sel) #6b222fff
    12532 
    12533 > color (#!8 & sel) #6d2330ff
    12534 
    12535 > color (#!8 & sel) #712432ff
    12536 
    12537 > color (#!8 & sel) #762634ff
    12538 
    12539 > color (#!8 & sel) #782735ff
    12540 
    12541 > color (#!8 & sel) #7c2837ff
    12542 
    12543 > color (#!8 & sel) #832a3aff
    12544 
    12545 > color (#!8 & sel) #872b3cff
    12546 
    12547 > color (#!8 & sel) #8a2c3dff
    12548 
    12549 > color (#!8 & sel) #8d2d3fff
    12550 
    12551 > color (#!8 & sel) #922f41ff
    12552 
    12553 > color (#!8 & sel) #963043ff
    12554 
    12555 > color (#!8 & sel) #9d3346ff
    12556 
    12557 > color (#!8 & sel) #a53549ff
    12558 
    12559 > color (#!8 & sel) #ac374cff
    12560 
    12561 > color (#!8 & sel) #b33a4fff
    12562 
    12563 > color (#!8 & sel) #b73b51ff
    12564 
    12565 > color (#!8 & sel) #ba3c52ff
    12566 
    12567 > color (#!8 & sel) #bd3d54ff
    12568 
    12569 > color (#!8 & sel) #bf3d55ff
    12570 
    12571 > color (#!8 & sel) #c23e56ff
    12572 
    12573 > color (#!8 & sel) #c43f57ff
    12574 
    12575 > color (#!8 & sel) #c74058ff
    12576 
    12577 > color (#!8 & sel) #ca4159ff
    12578 
    12579 > color (#!8 & sel) #cb415aff
    12580 
    12581 > color (#!8 & sel) #ce425cff
    12582 
    12583 > color (#!8 & sel) #d0435cff
    12584 
    12585 > color (#!8 & sel) #d4445eff
    12586 
    12587 > color (#!8 & sel) #d6455fff
    12588 
    12589 [Repeated 1 time(s)]
    12590 
    12591 > color (#!8 & sel) #d7455fff
    12592 
    12593 > color (#!8 & sel) #d6455fff
    12594 
    12595 > color (#!8 & sel) #d5445fff
    12596 
    12597 > color (#!8 & sel) #d1435dff
    12598 
    12599 > color (#!8 & sel) #cf425cff
    12600 
    12601 > color (#!8 & sel) #cd425bff
    12602 
    12603 > color (#!8 & sel) #cc425bff
    12604 
    12605 > color (#!8 & sel) #ca415aff
    12606 
    12607 > select #8/A
    12608 
    12609 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    12610 
    12611 > color (#!8 & sel) #ca4159ff
    12612 
    12613 > color (#!8 & sel) #bb3c53ff
    12614 
    12615 > color (#!8 & sel) #ac374cff
    12616 
    12617 > color (#!8 & sel) #a63549ff
    12618 
    12619 > color (#!8 & sel) #9d3245ff
    12620 
    12621 > color (#!8 & sel) #8e2e3fff
    12622 
    12623 > color (#!8 & sel) #852b3bff
    12624 
    12625 > color (#!8 & sel) #7c2837ff
    12626 
    12627 > color (#!8 & sel) #752634ff
    12628 
    12629 > color (#!8 & sel) #722533ff
    12630 
    12631 > color (#!8 & sel) #6e2331ff
    12632 
    12633 > color (#!8 & sel) #69222fff
    12634 
    12635 > color (#!8 & sel) #65212dff
    12636 
    12637 > color (#!8 & sel) #621f2bff
    12638 
    12639 > color (#!8 & sel) #601f2bff
    12640 
    12641 > color (#!8 & sel) #5e1e2aff
    12642 
    12643 > color (#!8 & sel) #5d1e29ff
    12644 
    12645 > color (#!8 & sel) #5c1e29ff
    12646 
    12647 > color (#!8 & sel) #5b1d29ff
    12648 
    12649 > color (#!8 & sel) #5a1d28ff
    12650 
    12651 > color (#!8 & sel) #591c27ff
    12652 
    12653 > color (#!8 & sel) #561c26ff
    12654 
    12655 [Repeated 1 time(s)]
    12656 
    12657 > color (#!8 & sel) #521a24ff
    12658 
    12659 > color (#!8 & sel) #511a24ff
    12660 
    12661 > select clear
    12662 
    12663 > select #8/C
    12664 
    12665 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    12666 
    12667 > color sel #521a24ff
    12668 
    12669 > color sel #8f2e3fff
    12670 
    12671 > color sel #af384eff
    12672 
    12673 > color sel #bb3c53ff
    12674 
    12675 > color sel #c84059ff
    12676 
    12677 > color sel #d6455fff
    12678 
    12679 > color sel #e14864ff
    12680 
    12681 > color sel #e84b67ff
    12682 
    12683 > color sel #ef4d6aff
    12684 
    12685 > color sel #f54f6cff
    12686 
    12687 > color sel #fc5170ff
    12688 
    12689 > color sel #ff5271ff
    12690 
    12691 [Repeated 1 time(s)]
    12692 
    12693 > color sel #f9506eff
    12694 
    12695 > color sel #f24e6bff
    12696 
    12697 > color sel #ef4d6aff
    12698 
    12699 [Repeated 1 time(s)]
    12700 
    12701 > color sel #ee4d6aff
    12702 
    12703 > color sel #e94b67ff
    12704 
    12705 > color sel #e54965ff
    12706 
    12707 > color sel #e54a66ff
    12708 
    12709 > color sel #ec4c69ff
    12710 
    12711 > color sel #ff5271ff
    12712 
    12713 [Repeated 1 time(s)]
    12714 
    12715 > color sel #ff5c6fff
    12716 
    12717 > color sel #ff6577ff
    12718 
    12719 > color sel #ff6a79ff
    12720 
    12721 > color sel #ff6c7cff
    12722 
    12723 > color sel #ff6e7eff
    12724 
    12725 > color sel #ff6f7fff
    12726 
    12727 > color sel #ff707fff
    12728 
    12729 > color sel #ff7180ff
    12730 
    12731 > color sel #ff7281ff
    12732 
    12733 > color sel #ff7282ff
    12734 
    12735 > color sel #ff7382ff
    12736 
    12737 > color sel #ff7482ff
    12738 
    12739 > color sel #ff7483ff
    12740 
    12741 > color sel #ff7582ff
    12742 
    12743 > color sel #ff7683ff
    12744 
    12745 > color sel #ff7883ff
    12746 
    12747 [Repeated 1 time(s)]
    12748 
    12749 > color sel #ff7a84ff
    12750 
    12751 > color sel #ff7b84ff
    12752 
    12753 [Repeated 1 time(s)]
    12754 
    12755 > color sel #ff7c84ff
    12756 
    12757 > color sel #ff7d85ff
    12758 
    12759 > color sel #ff7d84ff
    12760 
    12761 > color sel #ff7d85ff
    12762 
    12763 > color sel #ff7e85ff
    12764 
    12765 > color sel #ff7f85ff
    12766 
    12767 > color sel #ff8086ff
    12768 
    12769 > color sel #ff8087ff
    12770 
    12771 > color sel #ff8187ff
    12772 
    12773 > color sel #ff8288ff
    12774 
    12775 > color sel #ff8489ff
    12776 
    12777 > color sel #ff868bff
    12778 
    12779 > color sel #ff898cff
    12780 
    12781 > color sel #ff8b8dff
    12782 
    12783 > color sel #ff8b8eff
    12784 
    12785 > color sel #ff8b8dff
    12786 
    12787 > color sel #ff8a8dff
    12788 
    12789 > color sel #ff898dff
    12790 
    12791 > color sel #ff888eff
    12792 
    12793 > color sel #ff878dff
    12794 
    12795 > color sel #ff838cff
    12796 
    12797 > color sel #ff828bff
    12798 
    12799 > color sel #ff808aff
    12800 
    12801 > color sel #ff7f8aff
    12802 
    12803 [Repeated 1 time(s)]
    12804 
    12805 > color sel #ff7e8aff
    12806 
    12807 > color sel #ff7d89ff
    12808 
    12809 > color sel #ff7c88ff
    12810 
    12811 > color sel #ff7a88ff
    12812 
    12813 > color sel #ff7a87ff
    12814 
    12815 > color sel #ff7986ff
    12816 
    12817 > color sel #ff7886ff
    12818 
    12819 [Repeated 1 time(s)]
    12820 
    12821 > color sel #ff7785ff
    12822 
    12823 > color sel #ff7484ff
    12824 
    12825 [Repeated 1 time(s)]
    12826 
    12827 > color sel #ff7282ff
    12828 
    12829 > color sel #ff7283ff
    12830 
    12831 > color sel #ff7282ff
    12832 
    12833 [Repeated 1 time(s)]
    12834 
    12835 > color sel #ff7381ff
    12836 
    12837 > color sel #ff737fff
    12838 
    12839 > color sel #ff737dff
    12840 
    12841 > color sel #ff737bff
    12842 
    12843 [Repeated 1 time(s)]
    12844 
    12845 > color sel #ff737aff
    12846 
    12847 [Repeated 1 time(s)]
    12848 
    12849 > color sel #ff7379ff
    12850 
    12851 > color sel #ff7378ff
    12852 
    12853 [Repeated 1 time(s)]
    12854 
    12855 > color sel #ff7377ff
    12856 
    12857 > color sel #ff7376ff
    12858 
    12859 [Repeated 1 time(s)]
    12860 
    12861 > color sel #ff7375ff
    12862 
    12863 > color sel #ff7374ff
    12864 
    12865 > color sel #ff7373ff
    12866 
    12867 > color sel #ff7473ff
    12868 
    12869 > color sel #ff7573ff
    12870 
    12871 > color sel #ff7672ff
    12872 
    12873 > color sel #ff7772ff
    12874 
    12875 [Repeated 1 time(s)]
    12876 
    12877 > color sel #ff7872ff
    12878 
    12879 > color sel #ff7772ff
    12880 
    12881 > color sel #ff7672ff
    12882 
    12883 > color sel #ff7372ff
    12884 
    12885 > color sel #ff7273ff
    12886 
    12887 > color sel #ff7275ff
    12888 
    12889 > color sel #ff7276ff
    12890 
    12891 > color sel #ff7277ff
    12892 
    12893 > color sel #ff7278ff
    12894 
    12895 [Repeated 1 time(s)]
    12896 
    12897 > color sel #ff7279ff
    12898 
    12899 > color sel #ff727aff
    12900 
    12901 [Repeated 1 time(s)]
    12902 
    12903 > color sel #ff727bff
    12904 
    12905 > color sel #ff727cff
    12906 
    12907 > color sel #ff727dff
    12908 
    12909 > color sel #ff737eff
    12910 
    12911 > color sel #ff737fff
    12912 
    12913 [Repeated 1 time(s)]
    12914 
    12915 > color sel #ff7380ff
    12916 
    12917 [Repeated 1 time(s)]
    12918 
    12919 > color sel #ff7381ff
    12920 
    12921 > color sel #ff7382ff
    12922 
    12923 [Repeated 1 time(s)]
    12924 
    12925 > color sel #ff7383ff
    12926 
    12927 > color sel #ff7485ff
    12928 
    12929 > color sel #ff7386ff
    12930 
    12931 > color sel #ff7488ff
    12932 
    12933 > color sel #ff7489ff
    12934 
    12935 > color sel #ff748aff
    12936 
    12937 > color sel #ff748bff
    12938 
    12939 [Repeated 1 time(s)]
    12940 
    12941 > color sel #ff748cff
    12942 
    12943 [Repeated 1 time(s)]
    12944 
    12945 > color sel #ff738dff
    12946 
    12947 > color sel #ff738eff
    12948 
    12949 > color sel #ff7390ff
    12950 
    12951 > color sel #ff7293ff
    12952 
    12953 > color sel #ff7294ff
    12954 
    12955 > color sel #ff7293ff
    12956 
    12957 > color sel #ff7292ff
    12958 
    12959 [Repeated 1 time(s)]
    12960 
    12961 > color sel #ff7392ff
    12962 
    12963 > select clear
    12964 
    12965 > select #8/B
    12966 
    12967 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    12968 
    12969 > color (#!8 & sel) #fe7392ff
    12970 
    12971 > color (#!8 & sel) #e96986ff
    12972 
    12973 > color (#!8 & sel) #b75369ff
    12974 
    12975 > color (#!8 & sel) #9c4659ff
    12976 
    12977 > color (#!8 & sel) #934254ff
    12978 
    12979 > color (#!8 & sel) #924254ff
    12980 
    12981 > color (#!8 & sel) #914153ff
    12982 
    12983 > color (#!8 & sel) #8c3f50ff
    12984 
    12985 > color (#!8 & sel) #843c4cff
    12986 
    12987 > color (#!8 & sel) #823b4aff
    12988 
    12989 > color (#!8 & sel) #813a4aff
    12990 
    12991 [Repeated 1 time(s)]
    12992 
    12993 > color (#!8 & sel) #954355ff
    12994 
    12995 > color (#!8 & sel) #b8536aff
    12996 
    12997 > color (#!8 & sel) #ba546aff
    12998 
    12999 > color (#!8 & sel) #bb546bff
    13000 
    13001 > color (#!8 & sel) #c1576eff
    13002 
    13003 > color (#!8 & sel) #c55971ff
    13004 
    13005 [Repeated 2 time(s)]
    13006 
    13007 > color (#!8 & sel) #c85a72ff
    13008 
    13009 > color (#!8 & sel) #c85a73ff
    13010 
    13011 > color (#!8 & sel) #ca5b74ff
    13012 
    13013 > color (#!8 & sel) #cd5c75ff
    13014 
    13015 > color (#!8 & sel) #cd5d76ff
    13016 
    13017 > color (#!8 & sel) #cc5c75ff
    13018 
    13019 > color (#!8 & sel) #ca5b74ff
    13020 
    13021 [Repeated 1 time(s)]
    13022 
    13023 > color (#!8 & sel) #cb5c75ff
    13024 
    13025 > color (#!8 & sel) #cc5c75ff
    13026 
    13027 > color (#!8 & sel) #cd5c75ff
    13028 
    13029 > color (#!8 & sel) #ce5d76ff
    13030 
    13031 > color (#!8 & sel) #cf5d77ff
    13032 
    13033 > color (#!8 & sel) #d05e77ff
    13034 
    13035 > color (#!8 & sel) #c1153cff
    13036 
    13037 > color (#!8 & sel) #bb3b50ff
    13038 
    13039 > select clear
    13040 
    13041 > select #8/A-C
    13042 
    13043 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    13044 
    13045 > color (#!8 & sel) #bb3c53ff
    13046 
    13047 [Repeated 1 time(s)]
    13048 
    13049 > color (#!8 & sel) #b43a50ff
    13050 
    13051 > color (#!8 & sel) #9c3245ff
    13052 
    13053 > color (#!8 & sel) #8e2e3fff
    13054 
    13055 > color (#!8 & sel) #8b2d3eff
    13056 
    13057 > color (#!8 & sel) #882c3cff
    13058 
    13059 > color (#!8 & sel) #832a3aff
    13060 
    13061 > color (#!8 & sel) #7b2837ff
    13062 
    13063 > color (#!8 & sel) #762634ff
    13064 
    13065 [Repeated 1 time(s)]
    13066 
    13067 > color (#!8 & sel) #67212eff
    13068 
    13069 > color (#!8 & sel) #611f2bff
    13070 
    13071 > color (#!8 & sel) #601f2aff
    13072 
    13073 > color (#!8 & sel) #5c1e29ff
    13074 
    13075 > color (#!8 & sel) #561c26ff
    13076 
    13077 > color (#!8 & sel) #521a25ff
    13078 
    13079 > color (#!8 & sel) #521a24ff
    13080 
    13081 > color (#!8 & sel) #4f1923ff
    13082 
    13083 > color (#!8 & sel) #4d1922ff
    13084 
    13085 > color (#!8 & sel) #4c1922ff
    13086 
    13087 > color (#!8 & sel) #4b1821ff
    13088 
    13089 > color (#!8 & sel) #4a1821ff
    13090 
    13091 > color (#!8 & sel) #481720ff
    13092 
    13093 > color (#!8 & sel) #40151dff
    13094 
    13095 > color (#!8 & sel) #3d141bff
    13096 
    13097 > color (#!8 & sel) #3b131aff
    13098 
    13099 > color (#!8 & sel) #351117ff
    13100 
    13101 > color (#!8 & sel) #2d0e14ff
    13102 
    13103 > color (#!8 & sel) #2c0e14ff
    13104 
    13105 > color (#!8 & sel) #280d12ff
    13106 
    13107 > color (#!8 & sel) #220b0fff
    13108 
    13109 > color (#!8 & sel) #1b090cff
    13110 
    13111 > color (#!8 & sel) #1c090cff
    13112 
    13113 > color (#!8 & sel) #300f15ff
    13114 
    13115 > color (#!8 & sel) #5e1e2aff
    13116 
    13117 > color (#!8 & sel) #712432ff
    13118 
    13119 > color (#!8 & sel) #7a2736ff
    13120 
    13121 > color (#!8 & sel) #802939ff
    13122 
    13123 > color (#!8 & sel) #8c2d3eff
    13124 
    13125 > color (#!8 & sel) #943042ff
    13126 
    13127 > color (#!8 & sel) #9c3245ff
    13128 
    13129 > color (#!8 & sel) #a13447ff
    13130 
    13131 > color (#!8 & sel) #a63549ff
    13132 
    13133 > color (#!8 & sel) #ab374cff
    13134 
    13135 > color (#!8 & sel) #af384eff
    13136 
    13137 [Repeated 1 time(s)]
    13138 
    13139 > color (#!8 & sel) #9a3244ff
    13140 
    13141 > color (#!8 & sel) #902e40ff
    13142 
    13143 > color (#!8 & sel) #8d2d3fff
    13144 
    13145 > color (#!8 & sel) #8c2d3eff
    13146 
    13147 > color (#!8 & sel) #832a3aff
    13148 
    13149 > color (#!8 & sel) #7f2938ff
    13150 
    13151 > select clear
    13152 
    13153 > select #8/B
    13154 
    13155 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    13156 
    13157 > color (#!8 & sel) #7f2938ff
    13158 
    13159 > color (#!8 & sel) #8e2e3fff
    13160 
    13161 > color (#!8 & sel) #9b3245ff
    13162 
    13163 > color (#!8 & sel) #a33448ff
    13164 
    13165 > color (#!8 & sel) #b1394eff
    13166 
    13167 > color (#!8 & sel) #b73b51ff
    13168 
    13169 > color (#!8 & sel) #b93b52ff
    13170 
    13171 > color (#!8 & sel) #ba3c52ff
    13172 
    13173 > color (#!8 & sel) #d84560ff
    13174 
    13175 > color (#!8 & sel) #ff5271ff
    13176 
    13177 > select clear
    13178 
    13179 > select #8/C
    13180 
    13181 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    13182 
    13183 > color sel #ff566bff
    13184 
    13185 > color sel #ff576bff
    13186 
    13187 > color sel #ff576cff
    13188 
    13189 > color sel #ff586dff
    13190 
    13191 > color sel #ff5a6fff
    13192 
    13193 > color sel #ff5c71ff
    13194 
    13195 > color sel #ff5e73ff
    13196 
    13197 > color sel #ff5f75ff
    13198 
    13199 > color sel #ff6277ff
    13200 
    13201 > color sel #ff6278ff
    13202 
    13203 > color sel #ff6479ff
    13204 
    13205 > color sel #ff647aff
    13206 
    13207 > color sel #ff657bff
    13208 
    13209 > color sel #ff667bff
    13210 
    13211 > color sel #ff667cff
    13212 
    13213 > color sel #ff677dff
    13214 
    13215 > color sel #ff687dff
    13216 
    13217 > color sel #ff697eff
    13218 
    13219 > color sel #ff6a80ff
    13220 
    13221 > color sel #ff6b80ff
    13222 
    13223 > color sel #ff6c82ff
    13224 
    13225 > color sel #ff6d82ff
    13226 
    13227 > color sel #ff7388ff
    13228 
    13229 > color sel #ff7389ff
    13230 
    13231 > color sel #ff758bff
    13232 
    13233 > color sel #ff778dff
    13234 
    13235 > color sel #ff788eff
    13236 
    13237 > color sel #ff7a90ff
    13238 
    13239 > color sel #ff7c92ff
    13240 
    13241 > color sel #ff7e95ff
    13242 
    13243 > color sel #ff7f95ff
    13244 
    13245 > color sel #ff8198ff
    13246 
    13247 > color sel #ff8298ff
    13248 
    13249 > color sel #ff8299ff
    13250 
    13251 > color sel #ff849bff
    13252 
    13253 > color sel #ff879eff
    13254 
    13255 > color sel #ff879fff
    13256 
    13257 > color sel #ff89a0ff
    13258 
    13259 > color sel #ff8aa2ff
    13260 
    13261 > color sel #ff8ba2ff
    13262 
    13263 > color sel #ff8ba3ff
    13264 
    13265 > color sel #ff8ca4ff
    13266 
    13267 > color sel #ff8da4ff
    13268 
    13269 > color sel #ff8fa7ff
    13270 
    13271 > color sel #ff90a8ff
    13272 
    13273 > color sel #ff91a9ff
    13274 
    13275 > color sel #ff91aaff
    13276 
    13277 > select clear
    13278 
    13279 > select #8/C
    13280 
    13281 1919 atoms, 1957 bonds, 229 residues, 1 model selected 
    13282 
    13283 > color sel #ff8fa7ff
    13284 
    13285 > select clear
    13286 
    13287 > undo
    13288 
    13289 > select clear
    13290 
    13291 > select #8/A-C
    13292 
    13293 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    13294 
    13295 > select #8/A
    13296 
    13297 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    13298 
    13299 > color (#!8 & sel) #c1153cff
    13300 
    13301 > color (#!8 & sel) #be3c51ff
    13302 
    13303 > color (#!8 & sel) #ba3a4fff
    13304 
    13305 > color (#!8 & sel) #a83548ff
    13306 
    13307 > color (#!8 & sel) #9c3142ff
    13308 
    13309 > color (#!8 & sel) #952f40ff
    13310 
    13311 > color (#!8 & sel) #8d2c3cff
    13312 
    13313 > color (#!8 & sel) #862a39ff
    13314 
    13315 > color (#!8 & sel) #852a39ff
    13316 
    13317 > color (#!8 & sel) #842938ff
    13318 
    13319 > color (#!8 & sel) #832938ff
    13320 
    13321 [Repeated 1 time(s)]
    13322 
    13323 > color (#!8 & sel) #812837ff
    13324 
    13325 > color (#!8 & sel) #802837ff
    13326 
    13327 > color (#!8 & sel) #802836ff
    13328 
    13329 > color (#!8 & sel) #792634ff
    13330 
    13331 > color (#!8 & sel) #782533ff
    13332 
    13333 > color (#!8 & sel) #762532ff
    13334 
    13335 > color (#!8 & sel) #742431ff
    13336 
    13337 > color (#!8 & sel) #702330ff
    13338 
    13339 > color (#!8 & sel) #6e232fff
    13340 
    13341 > color (#!8 & sel) #6d222fff
    13342 
    13343 > color (#!8 & sel) #6c222eff
    13344 
    13345 [Repeated 1 time(s)]
    13346 
    13347 > color (#!8 & sel) #6d222eff
    13348 
    13349 > color (#!8 & sel) #6e232fff
    13350 
    13351 > color (#!8 & sel) #6f232fff
    13352 
    13353 > color (#!8 & sel) #702330ff
    13354 
    13355 [Repeated 1 time(s)]
    13356 
    13357 > select clear
    13358 
    13359 > select #8/A
    13360 
    13361 1565 atoms, 1597 bonds, 1 pseudobond, 188 residues, 2 models selected 
    13362 
    13363 > color (#!8 & sel) #c1153cff
    13364 
    13365 > color (#!8 & sel) #be3c51ff
    13366 
    13367 > color (#!8 & sel) #be3b51ff
    13368 
    13369 > color (#!8 & sel) #b3384cff
    13370 
    13371 > color (#!8 & sel) #a63447ff
    13372 
    13373 > color (#!8 & sel) #9d3143ff
    13374 
    13375 > color (#!8 & sel) #942e3fff
    13376 
    13377 > color (#!8 & sel) #902d3dff
    13378 
    13379 > color (#!8 & sel) #8a2b3bff
    13380 
    13381 > color (#!8 & sel) #802836ff
    13382 
    13383 > color (#!8 & sel) #772533ff
    13384 
    13385 > color (#!8 & sel) #702330ff
    13386 
    13387 > color (#!8 & sel) #6b222eff
    13388 
    13389 > color (#!8 & sel) #67202cff
    13390 
    13391 > color (#!8 & sel) #641f2bff
    13392 
    13393 > color (#!8 & sel) #631f2aff
    13394 
    13395 [Repeated 1 time(s)]
    13396 
    13397 > color (#!8 & sel) #611e29ff
    13398 
    13399 > color (#!8 & sel) #5d1d27ff
    13400 
    13401 > color (#!8 & sel) #581c25ff
    13402 
    13403 > color (#!8 & sel) #571b25ff
    13404 
    13405 [Repeated 1 time(s)]
    13406 
    13407 > color (#!8 & sel) #591c26ff
    13408 
    13409 > color (#!8 & sel) #5c1d27ff
    13410 
    13411 > color (#!8 & sel) #611e29ff
    13412 
    13413 > color (#!8 & sel) #67202cff
    13414 
    13415 > color (#!8 & sel) #712330ff
    13416 
    13417 > color (#!8 & sel) #742432ff
    13418 
    13419 > color (#!8 & sel) #752532ff
    13420 
    13421 > color (#!8 & sel) #722431ff
    13422 
    13423 > color (#!8 & sel) #712430ff
    13424 
    13425 > color (#!8 & sel) #702330ff
    13426 
    13427 [Repeated 1 time(s)]
    13428 
    13429 > color (#!8 & sel) #6d222fff
    13430 
    13431 > color (#!8 & sel) #6c222eff
    13432 
    13433 [Repeated 1 time(s)]
    13434 
    13435 > color (#!8 & sel) #6b222eff
    13436 
    13437 [Repeated 1 time(s)]
    13438 
    13439 > color (#!8 & sel) #6b212dff
    13440 
    13441 > color (#!8 & sel) #6a212dff
    13442 
    13443 [Repeated 2 time(s)]
    13444 
    13445 > color (#!8 & sel) #69212dff
    13446 
    13447 [Repeated 1 time(s)]
    13448 
    13449 > select clear
    13450 
    13451 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    13452 
    13453 > select #8/A-C
    13454 
    13455 5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected 
    13456 Alignment identifier is 1 
    13457 
    13458 > select #8/C:469
    13459 
    13460 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13461 
    13462 > select #8/C:469-473
    13463 
    13464 48 atoms, 47 bonds, 5 residues, 1 model selected 
    13465 
    13466 > select #8/C:475
    13467 
    13468 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13469 
    13470 > select #8/C:475-485
    13471 
    13472 92 atoms, 92 bonds, 11 residues, 1 model selected 
    13473 
    13474 > select #8/A-C:491
    13475 
    13476 21 atoms, 18 bonds, 3 residues, 1 model selected 
    13477 
    13478 > select #8/A-C:491-572
    13479 
    13480 2013 atoms, 2049 bonds, 246 residues, 1 model selected 
    13481 
    13482 > select clear
    13483 
    13484 > view name front
    13485 
    13486 > rotate 90 y
    13487 
    13488 Unknown command: rotate 90 y 
    13489 
    13490 > rotate y 90
    13491 
    13492 Unknown command: rotate y 90 
    13493 
    13494 > rotate
    13495 
    13496 Unknown command: rotate 
    13497 
    13498 > turn y 90
    13499 
    13500 > turn z 90
    13501 
    13502 > turn x 90
    13503 
    13504 > view front
    13505 
    13506 > ui tool show "Side View"
    13507 
    13508 > view name front
    13509 
    13510 > turn x 90
    13511 
    13512 > view front
    13513 
    13514 > turn x 90
    13515 
    13516 > view name front
    13517 
    13518 [Repeated 1 time(s)]
    13519 
    13520 > turn x 90
    13521 
    13522 > hide #!8 models
    13523 
    13524 > transparency #2,3,7 0
    13525 
    13526 > transparency #2,3,7 70
    13527 
    13528 > movie record size info
    13529 
    13530 Invalid "size" argument: Expected an integer 
    13531 
    13532 > lighting soft
    13533 
    13534 > save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true
    13535 
    13536 ——— End of log from Mon Jun 9 23:00:16 2025 ———
    13537 
    13538 opened ChimeraX session 
    13539 
    13540 > view front
    13541 
    13542 > transparency #2,3,7 40
    13543 
    13544 > transparency #2,3,7 60
    13545 
    13546 > transparency #2,3,7 80
    13547 
    13548 > transparency #2,3,7 30
    13549 
    13550 > transparency #2,3,7 10
    13551 
    13552 > view front
    13553 
    13554 > graphics silhouettes true
    13555 
    13556 > lighting depthCue false
    13557 
    13558 > lighting soft
    13559 
    13560 > graphics bgColor white
    13561 
    13562 > show #!8 models
    13563 
    13564 > hide #!8 models
    13565 
    13566 > show #!8 models
    13567 
    13568 > hide #!8 models
    13569 
    13570 > transparency #2 10
    13571 
    13572 > transparency #2 0
    13573 
    13574 > transparency #3 0
    13575 
    13576 > transparency #7 0
    13577 
    13578 > transparency #7 60
    13579 
    13580 > hide #!8 models
    13581 
    13582 > transparency #7 0
    13583 
    13584 > transparency #3 30
    13585 
    13586 > transparency #3 50
    13587 
    13588 > transparency #3 10
    13589 
    13590 > show #!8 models
    13591 
    13592 > hide #!8 models
    13593 
    13594 > transparency #3,2,7 10
    13595 
    13596 > lightling gent;le
    13597 
    13598 Unknown command: lightling gent;le 
    13599 
    13600 > lightling gente
    13601 
    13602 Unknown command: lightling gente 
    13603 
    13604 > lightling gentle
    13605 
    13606 Unknown command: lightling gentle 
    13607 
    13608 > lighting gentle
    13609 
    13610 > transparency #3,2,7 60
    13611 
    13612 > show #!8 models
    13613 
    13614 > transparency #3,2,7 50
    13615 
    13616 > transparency #3,2,7 65
    13617 
    13618 > lighting soft
    13619 
    13620 > transparency #3,2,7 68
    13621 
    13622 > lighting gentle
    13623 
    13624 > view frony
    13625 
    13626 Expected an objects specifier or a view name or a keyword 
    13627 
    13628 > view front
    13629 
    13630 > hide #!8 models
    13631 
    13632 > transparency #3,2,7 0
    13633 
    13634 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    13635 > supersample 4 transparentBackground true
    13636 
    13637 [Repeated 1 time(s)]
    13638 
    13639 > transparency #3,2,7 68
    13640 
    13641 > show #!8 models
    13642 
    13643 > view name front
    13644 
    13645 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    13646 > supersample 4
    13647 
    13648 > color #7 #8c8dfcff models
    13649 
    13650 > color #3 #8c8dfcff models
    13651 
    13652 > color #2 #8c8dfcff models
    13653 
    13654 > transparency #3,2,7 68
    13655 
    13656 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    13657 > supersample 4
    13658 
    13659 > hide #!8 models
    13660 
    13661 > transparency #3,2,7 0
    13662 
    13663 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    13664 > supersample 4 transparentBackground true
    13665 
    13666 > color #3 #a3a7ffff models
    13667 
    13668 > color #2 #a3a7ffff models
    13669 
    13670 > color #7 #a3a7ffff models
    13671 
    13672 > color #7 #b5bcffff models
    13673 
    13674 > color #3 #b5bcffff models
    13675 
    13676 > color #2 #b5bcffff models
    13677 
    13678 > color #2 #7a81ffff models
    13679 
    13680 > color #3 #7a81ffff models
    13681 
    13682 > transparency #3,2,7 68
    13683 
    13684 > transparency #3,2,7 0
    13685 
    13686 > transparency #3,2,7 68
    13687 
    13688 > show #!8 models
    13689 
    13690 > color #7 #c4caffff models
    13691 
    13692 > transparency #3,2,7 0
    13693 
    13694 > color #3 #919affff models
    13695 
    13696 > color #7 #7a81ffff models
    13697 
    13698 > color #7 #919affff models
    13699 
    13700 > color #2 #919affff models
    13701 
    13702 > color #7 #a8b2ffff models
    13703 
    13704 > color #3 #a8b2ffff models
    13705 
    13706 > color #2 #a8b2ffff models
    13707 
    13708 > transparency #3,2,7 68
    13709 
    13710 > transparency #3,2,7 0
    13711 
    13712 > transparency #3,2,7 68
    13713 
    13714 > transparency #3,2,7 0
    13715 
    13716 > hide #!8 models
    13717 
    13718 > save /Users/ConstantinePetridis/Desktop/Cap.png width 4000 height 2498
    13719 > supersample 4 transparentBackground true
    13720 
    13721 > transparency #3,2,7 68
    13722 
    13723 > show #!8 models
    13724 
    13725 > transparency #3,2,7 69
    13726 
    13727 > transparency #3,2,7 70
    13728 
    13729 > save /Users/ConstantinePetridis/Desktop/Cap2.png width 4000 height 2498
    13730 > supersample 4
    13731 
    13732 > transparency #3,2,7 20
    13733 
    13734 > transparency #3,2,7 30
    13735 
    13736 > usage vop
    13737 
    13738 vop [optional] 
    13739 — alias of "volume $*" 
    13740 optional: the rest of line 
    13741 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    13742 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    13743 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    13744 a number] [transparency a number] [appearance appearance] [nameAppearance a
    13745 text string] [nameForget nameForget] [step map step] [region map region]
    13746 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    13747 floats] [voxelSize 1 or 3 floats] [planes planes
    13748 x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
    13749 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    13750 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    13751 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    13752 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    13753 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    13754 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    13755 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    13756 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    13757 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    13758 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    13759 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    13760 [fullRegionOnGpu true or false] [btCorrection true or false]
    13761 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    13762 false] [linearInterpolation true or false] [dimTransparency true or false]
    13763 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    13764 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    13765 [subdivideSurface true or false] [subdivisionLevels an integer]
    13766 [surfaceSmoothing true or false] [smoothingIterations an integer]
    13767 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    13768 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    13769 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    13770 an integer] [backingColor backingColor] 
    13771 — set volume model parameters, display style and colors 
    13772 style: one of image, mesh, solid, or surface 
    13773 change: one of image or surface 
    13774 close: one of image or surface 
    13775 level: some numbers, repeatable 
    13776 rmsLevel: some numbers, repeatable 
    13777 sdLevel: some numbers, repeatable 
    13778 encloseVolume: some numbers 
    13779 fastEncloseVolume: some numbers 
    13780 color: a color, repeatable 
    13781 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    13782 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    13783 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    13784 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    13785 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    13786 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    13787 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    13788 Bone 
    13789 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    13790 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    13791 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    13792 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    13793 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    13794 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    13795 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    13796 Bone 
    13797 orthoplanes: one of off, xy, xyz, xz, or yz 
    13798 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    13799 initialColors: some colors 
    13800 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    13801 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    13802 rgba12, rgba16, rgba4, or rgba8 
    13803 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    13804 planeSpacing: one of max, mean, or min or a number 
    13805 positionPlanes: 3-tuple of integers 
    13806 backingColor: a color or none 
    13807 Subcommands are:
    13808 
    13809   * volume add
    13810   * volume bin
    13811   * volume boxes
    13812   * volume channels
    13813   * volume copy
    13814   * volume cover
    13815   * volume defaultvalues
    13816   * volume erase
    13817   * volume falloff
    13818   * volume flatten
    13819   * volume flip
    13820   * volume fourier
    13821   * volume gaussian
    13822   * volume laplacian
    13823   * volume localCorrelation
    13824   * volume mask
    13825   * volume maximum
    13826   * volume median
    13827   * volume minimum
    13828   * volume morph
    13829   * volume multiply
    13830   * volume new
    13831   * volume octant
    13832   * volume ~octant
    13833   * volume onesmask
    13834   * volume permuteAxes
    13835   * volume resample
    13836   * volume ridges
    13837   * volume scale
    13838   * volume settings
    13839   * volume sharpen
    13840   * volume splitbyzone
    13841   * volume subtract
    13842   * volume threshold
    13843   * volume tile
    13844   * volume unbend
    13845   * volume unroll
    13846   * volume unzone
    13847   * volume zone
    13848 
    13849  
    13850 
    13851 > hide #!7 models
    13852 
    13853 > show #!7 models
    13854 
    13855 > hide #!3 models
    13856 
    13857 > show #!3 models
    13858 
    13859 > vop copy #3
    13860 
    13861 Opened emd_51808.map copy as #9, grid size 500,500,500, pixel 1.35, shown at
    13862 step 1, values float32 
    13863 
    13864 > show #!3 models
    13865 
    13866 > hide #!3 models
    13867 
    13868 > show #!3 models
    13869 
    13870 > hide #!3 models
    13871 
    13872 > show #!3 models
    13873 
    13874 > hide #!3 models
    13875 
    13876 > usage vop
    13877 
    13878 vop [optional] 
    13879 — alias of "volume $*" 
    13880 optional: the rest of line 
    13881 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    13882 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    13883 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    13884 a number] [transparency a number] [appearance appearance] [nameAppearance a
    13885 text string] [nameForget nameForget] [step map step] [region map region]
    13886 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    13887 floats] [voxelSize 1 or 3 floats] [planes planes
    13888 x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
    13889 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    13890 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    13891 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    13892 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    13893 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    13894 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    13895 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    13896 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    13897 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    13898 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    13899 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    13900 [fullRegionOnGpu true or false] [btCorrection true or false]
    13901 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    13902 false] [linearInterpolation true or false] [dimTransparency true or false]
    13903 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    13904 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    13905 [subdivideSurface true or false] [subdivisionLevels an integer]
    13906 [surfaceSmoothing true or false] [smoothingIterations an integer]
    13907 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    13908 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    13909 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    13910 an integer] [backingColor backingColor] 
    13911 — set volume model parameters, display style and colors 
    13912 style: one of image, mesh, solid, or surface 
    13913 change: one of image or surface 
    13914 close: one of image or surface 
    13915 level: some numbers, repeatable 
    13916 rmsLevel: some numbers, repeatable 
    13917 sdLevel: some numbers, repeatable 
    13918 encloseVolume: some numbers 
    13919 fastEncloseVolume: some numbers 
    13920 color: a color, repeatable 
    13921 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    13922 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    13923 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    13924 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    13925 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    13926 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    13927 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    13928 Bone 
    13929 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    13930 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    13931 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    13932 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    13933 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    13934 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    13935 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    13936 Bone 
    13937 orthoplanes: one of off, xy, xyz, xz, or yz 
    13938 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    13939 initialColors: some colors 
    13940 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    13941 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    13942 rgba12, rgba16, rgba4, or rgba8 
    13943 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    13944 planeSpacing: one of max, mean, or min or a number 
    13945 positionPlanes: 3-tuple of integers 
    13946 backingColor: a color or none 
    13947 Subcommands are:
    13948 
    13949   * volume add
    13950   * volume bin
    13951   * volume boxes
    13952   * volume channels
    13953   * volume copy
    13954   * volume cover
    13955   * volume defaultvalues
    13956   * volume erase
    13957   * volume falloff
    13958   * volume flatten
    13959   * volume flip
    13960   * volume fourier
    13961   * volume gaussian
    13962   * volume laplacian
    13963   * volume localCorrelation
    13964   * volume mask
    13965   * volume maximum
    13966   * volume median
    13967   * volume minimum
    13968   * volume morph
    13969   * volume multiply
    13970   * volume new
    13971   * volume octant
    13972   * volume ~octant
    13973   * volume onesmask
    13974   * volume permuteAxes
    13975   * volume resample
    13976   * volume ridges
    13977   * volume scale
    13978   * volume settings
    13979   * volume sharpen
    13980   * volume splitbyzone
    13981   * volume subtract
    13982   * volume threshold
    13983   * volume tile
    13984   * volume unbend
    13985   * volume unroll
    13986   * volume unzone
    13987   * volume zone
    13988 
    13989  
    13990 
    13991 > volume zone #9 nearAtoms #8
    13992 
    13993 > hide #!7 models
    13994 
    13995 > hide #!2 models
    13996 
    13997 > show #!3 models
    13998 
    13999 > show #!2 models
    14000 
    14001 > usage vop
    14002 
    14003 vop [optional] 
    14004 — alias of "volume $*" 
    14005 optional: the rest of line 
    14006 volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
    14007 close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
    14008 encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
    14009 a number] [transparency a number] [appearance appearance] [nameAppearance a
    14010 text string] [nameForget nameForget] [step map step] [region map region]
    14011 [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
    14012 floats] [voxelSize 1 or 3 floats] [planes planes
    14013 x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
    14014 [pickable true or false] [calculateSurfaces true or false] [boxFaces true or
    14015 false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
    14016 imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
    14017 floats] [axis an axis vector] [coordinateSystem a coordinate-system]
    14018 [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
    14019 number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
    14020 initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
    14021 [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
    14022 false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
    14023 true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
    14024 [projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
    14025 [fullRegionOnGpu true or false] [btCorrection true or false]
    14026 [minimalTextureMemory true or false] [maximumIntensityProjection true or
    14027 false] [linearInterpolation true or false] [dimTransparency true or false]
    14028 [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
    14029 true or false] [twoSidedLighting true or false] [flipNormals true or false]
    14030 [subdivideSurface true or false] [subdivisionLevels an integer]
    14031 [surfaceSmoothing true or false] [smoothingIterations an integer]
    14032 [smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
    14033 [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
    14034 [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
    14035 an integer] [backingColor backingColor] 
    14036 — set volume model parameters, display style and colors 
    14037 style: one of image, mesh, solid, or surface 
    14038 change: one of image or surface 
    14039 close: one of image or surface 
    14040 level: some numbers, repeatable 
    14041 rmsLevel: some numbers, repeatable 
    14042 sdLevel: some numbers, repeatable 
    14043 encloseVolume: some numbers 
    14044 fastEncloseVolume: some numbers 
    14045 color: a color, repeatable 
    14046 appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    14047 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    14048 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    14049 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    14050 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    14051 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    14052 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    14053 Bone 
    14054 nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
    14055 Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
    14056 CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
    14057 Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
    14058 Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
    14059 Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
    14060 White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
    14061 Bone 
    14062 orthoplanes: one of off, xy, xyz, xz, or yz 
    14063 imageMode: one of box faces, full region, orthoplanes, or tilted slab 
    14064 initialColors: some colors 
    14065 colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
    14066 la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
    14067 rgba12, rgba16, rgba4, or rgba8 
    14068 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays 
    14069 planeSpacing: one of max, mean, or min or a number 
    14070 positionPlanes: 3-tuple of integers 
    14071 backingColor: a color or none 
    14072 Subcommands are:
    14073 
    14074   * volume add
    14075   * volume bin
    14076   * volume boxes
    14077   * volume channels
    14078   * volume copy
    14079   * volume cover
    14080   * volume defaultvalues
    14081   * volume erase
    14082   * volume falloff
    14083   * volume flatten
    14084   * volume flip
    14085   * volume fourier
    14086   * volume gaussian
    14087   * volume laplacian
    14088   * volume localCorrelation
    14089   * volume mask
    14090   * volume maximum
    14091   * volume median
    14092   * volume minimum
    14093   * volume morph
    14094   * volume multiply
    14095   * volume new
    14096   * volume octant
    14097   * volume ~octant
    14098   * volume onesmask
    14099   * volume permuteAxes
    14100   * volume resample
    14101   * volume ridges
    14102   * volume scale
    14103   * volume settings
    14104   * volume sharpen
    14105   * volume splitbyzone
    14106   * volume subtract
    14107   * volume threshold
    14108   * volume tile
    14109   * volume unbend
    14110   * volume unroll
    14111   * volume unzone
    14112   * volume zone
    14113 
    14114  
    14115 
    14116 > vop copy #3
    14117 
    14118 Opened emd_51808.map copy as #10, grid size 500,500,500, pixel 1.35, shown at
    14119 step 1, values float32 
    14120 
    14121 > vop subtract #10 #9
    14122 
    14123 Opened volume difference as #11, grid size 500,500,500, pixel 1.35, shown at
    14124 step 1, values float32 
    14125 
    14126 > show #!10 models
    14127 
    14128 > hide #!10 models
    14129 
    14130 > hide #!2 models
    14131 
    14132 > show #!2 models
    14133 
    14134 > show #!3 models
    14135 
    14136 > hide #!3 models
    14137 
    14138 > show #!7 models
    14139 
    14140 > show #!9 models
    14141 
    14142 > hide #!9 models
    14143 
    14144 > show #!9 models
    14145 
    14146 > show #!10 models
    14147 
    14148 > hide #!9 models
    14149 
    14150 > show #!9 models
    14151 
    14152 > hide #!9 models
    14153 
    14154 > hide #!11 models
    14155 
    14156 > show #!11 models
    14157 
    14158 > hide #!10 models
    14159 
    14160 > select add #11
    14161 
    14162 2 models selected 
    14163 
    14164 > select subtract #11
    14165 
    14166 Nothing selected 
    14167 
    14168 > select add #11
    14169 
    14170 2 models selected 
    14171 
    14172 > select subtract #11
    14173 
    14174 Nothing selected 
    14175 
    14176 > hide #11.1 models
    14177 
    14178 > show #11.1 models
    14179 
    14180 > hide #!11 models
    14181 
    14182 > show #!11 models
    14183 
    14184 > volume #11 level -0.2366
    14185 
    14186 > volume #11 level -0.8872
    14187 
    14188 > close #11
    14189 
    14190 > show #!10 models
    14191 
    14192 > volume zone #9 nearAtoms #8 invert true
    14193 
    14194 volume zone command currently does not support invert True with newMap False 
    14195 
    14196 > volume zone #9 nearAtoms #8 invert true newMap true
    14197 
    14198 Opened emd_51808.map copy zone as #11, grid size 500,500,500, pixel 1.35,
    14199 shown at step 1, values float32 
    14200 
    14201 > hide #!7 models
    14202 
    14203 > hide #!2 models
    14204 
    14205 > show #!2 models
    14206 
    14207 > show #!3 models
    14208 
    14209 > hide #!3 models
     1648[deleted to fit within ticket limits]
     1649
    142101650
    142111651> show #!7 models