Changes between Initial Version and Version 1 of Ticket #7348


Ignore:
Timestamp:
Aug 1, 2022, 9:25:47 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #7348

    • Property Component Unassigned → Depiction
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → KeyError deleting 2D arrow

  • Ticket #7348 – Description

    initial v1  
    19861986> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    19871987
    1988 > volume #1 region 0,0,0,1385,1409,1604
    1989 
    1990 > volume #1 region all
    1991 
    1992 > volume #1 region 0,0,0,2129,1523,1748
    1993 
    1994 > view orient
    1995 
    1996 > zoom 0.85
    1997 
    1998 > view name p1
    1999 
    2000 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2001 
    2002 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2003 shown at step 1, values int8 
    2004 
    2005 > close #2
    2006 
    2007 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    2008 
    2009 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2010 shown at step 1, values int8 
    2011 
    2012 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    2013 
    2014 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2015 shown at step 1, values int8 
    2016 
    2017 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2018 
    2019 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2020 shown at step 1, values int8 
    2021 
    2022 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    2023 
    2024 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2025 shown at step 1, values int8 
    2026 
    2027 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2028 
    2029 > volume #2 show style surface level 0.8 color #5555ff
    2030 
    2031 > volume #1 region 0,0,0,2129,1523,1740
    2032 
    2033 > volume all region 0,0,0,2129,1523,1740
    2034 
    2035 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2036 > showOutlineBox true imageMode "box faces"
    2037 
    2038 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2039 > showOutlineBox true imageMode "box faces"
    2040 
    2041 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2042 > showOutlineBox true imageMode "box faces"
    2043 
    2044 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    2045 > faces"
    2046 
    2047 > volume #2 show style surface level -50 color #5555ff
    2048 
    2049 > volume #2 show style surface level 10 color #5555ff
    2050 
    2051 > lighting soft
    2052 
    2053 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2054 
    2055 > volume #2 show style surface level 0.8 color #5555ff
    2056 
    2057 > volume #3 show style surface level 0.8 color #aa557f
    2058 
    2059 > volume #4 show style surface level 0.8 color #f514fd
    2060 
    2061 > volume #5 show style surface level 0.8 color #11ffcc
    2062 
    2063 > ~display #1
    2064 
    2065 > volume #2 transparency 0.6
    2066 
    2067 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2068 
    2069 > display #1
    2070 
    2071 > volume all region 0,0,0,2129,1523,1744
    2072 
    2073 > ~display #1
    2074 
    2075 > volume #2 show style surface step 2
    2076 
    2077 > volume #3 show style surface step 3
    2078 
    2079 > volume #4 show style surface step 2
    2080 
    2081 > volume #5 show style surface step 2
    2082 
    2083 > volume #5 show style surface step 1
    2084 
    2085 > volume #5 show style surface step 2
    2086 
    2087 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2088 
    2089 > view name p2
    2090 
    2091 > view list
    2092 
    2093 Named views: p1, p2 
    2094 
    2095 > view p1
    2096 
    2097 > view p2
    2098 
    2099 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2100 
    2101 > fly p2 p1 100
    2102 
    2103 > wait
    2104 
    2105 > view p2
    2106 
    2107 > display #1
    2108 
    2109 > volume #1 region 0,0,0,2129,1523,1744
    2110 
    2111 > volume #1 region 0,0,0,2129,1523,1740
    2112 
    2113 > volume #1 region 0,0,0,2129,1523,1742
    2114 
    2115 > volume #1 region 0,0,0,2129,1523,1743
    2116 
    2117 > volume #1 region 0,0,0,2129,1523,1744
    2118 
    2119 > volume #1 region 0,0,0,2129,1523,1743
    2120 
    2121 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2122 
    2123 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    2124 
    2125 opened ChimeraX session 
    2126 
    2127 > display #1
    2128 
    2129 > ~display #2-5
    2130 
    2131 > display #2-5
    2132 
    2133 > ~display #1
    2134 
    2135 > display #1
    2136 
    2137 > ~display #2-5
    2138 
    2139 > volume all region 0,0,0,2129,1523,1743
    2140 
    2141 > display #2-5
    2142 
    2143 > view p2
    2144 
    2145 > lighting soft
    2146 
    2147 > view p1
    2148 
    2149 > help hide
    2150 
    2151 > hide #1
    2152 
    2153 > view p2
    2154 
    2155 > show #2
    2156 
    2157 > volume #2-5 show style surface
    2158 
    2159 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2160 
    2161 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    2162 
    2163 opened ChimeraX session 
    2164 
    2165 > display #1
    2166 
    2167 > ~display #2-5
    2168 
    2169 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2170 
    2171 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    2172 
    2173 opened ChimeraX session 
    2174 
    2175 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    2176 
    2177 > movie record supersample 3
    2178 
    2179 > fly p2 p1 100
    2180 
    2181 > wait
    2182 
    2183 > volume #2-5 show style surface transparency 0.5
    2184 
    2185 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    2186 > bgColor black margin 5
    2187 
    2188 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    2189 > bgColor black margin 5
    2190 
    2191 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    2192 > true bgColor black margin 5
    2193 
    2194 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    2195 > true bgColor black margin 5
    2196 
    2197 > volume all planes z,1743,30
    2198 
    2199 > wait 1743
    2200 
    2201 > volume #1 hide
    2202 
    2203 > wait 1
    2204 
    2205 > volume #2-5 region all
    2206 
    2207 > wait 1
    2208 
    2209 > volume #3-5 transparency 0
    2210 
    2211 > volume #2 transparency 0.6
    2212 
    2213 > roll y 1 360
    2214 
    2215 > wait
    2216 
    2217 > fly p1 p2 100
    2218 
    2219 > wait
    2220 
    2221 > perframe "volume all region 0,0,0,2129,1523,$1" ranges 1743,30
    2222 
    2223 > wait 1720
    2224 
    2225 > movie encode framerate 25 quality good output
    2226 > /tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4 verbose true
    2227 > format h264 wait true
    2228 
    2229 /usr/libexec/UCSF-ChimeraX/bin/ffmpeg -r 25.0 -i /tmp/chimovie_mNsA-%05d.ppm
    2230 -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4
    2231 -pix_fmt yuv420p -crf 20
    2232 /tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4 
    2233 stdout: 
    2234  
    2235 stderr: 
    2236 ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers 
    2237 built with gcc 8 (GCC) 
    2238 configuration: --prefix=/tmp/chx-v1.4.jOWCxR/build --enable-gpl --enable-
    2239 version3 --disable-network --disable-doc --disable-devices --disable-ffplay
    2240 --disable-ffserver --disable-ffprobe --enable-libtheora --enable-libvpx
    2241 --enable-libx264 --yasmexe=/tmp/chx-v1.4.jOWCxR/build/bin/yasm --optflags=-O
    2242 --extra-cflags=-I/tmp/chx-v1.4.jOWCxR/build/include --extra-ldflags='-O3 -Wall
    2243 -Wextra -D_FORTIFY=2 -L/tmp/chx-v1.4.jOWCxR/build/lib' --extra-libs=-ldl 
    2244 libavutil 55. 34.101 / 55. 34.101 
    2245 libavcodec 57. 64.101 / 57. 64.101 
    2246 libavformat 57. 56.101 / 57. 56.101 
    2247 libavdevice 57. 1.100 / 57. 1.100 
    2248 libavfilter 6. 65.100 / 6. 65.100 
    2249 libswscale 4. 2.100 / 4. 2.100 
    2250 libswresample 2. 3.100 / 2. 3.100 
    2251 libpostproc 54. 1.100 / 54. 1.100 
    2252 Input #0, image2, from '/tmp/chimovie_mNsA-%05d.ppm': 
    2253 Duration: 00:02:41.16, start: 0.000000, bitrate: N/A 
    2254 Stream #0:0: Video: ppm, rgb24, 1708x1033, 25 tbr, 25 tbn, 25 tbc 
    2255 [libx264 @ 0x2f41260] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
    2256 FMA3 AVX2 LZCNT BMI2 
    2257 [libx264 @ 0x2f41260] profile High, level 4.0 
    2258 [libx264 @ 0x2f41260] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
    2259 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
    2260 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
    2261 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
    2262 fast_pskip=1 chroma_qp_offset=-2 threads=32 lookahead_threads=5
    2263 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
    2264 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
    2265 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
    2266 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
    2267 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 
    2268 Output #0, mp4, to
    2269 '/tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4': 
    2270 Metadata: 
    2271 encoder : Lavf57.56.101 
    2272 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
    2273 1708x1032, q=-1--1, 25 fps, 12800 tbn, 25 tbc 
    2274 Metadata: 
    2275 encoder : Lavc57.64.101 libx264 
    2276 Side data: 
    2277 cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 
    2278 Stream mapping: 
    2279 Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) 
    2280 Press [q] to stop, [?] for help 
    2281 frame= 74 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
    2282 frame= 156 fps=155 q=25.0 size= 1664kB time=00:00:03.08 bitrate=4426.1kbits/s
    2283 speed=3.06x frame= 230 fps=152 q=25.0 size= 6025kB time=00:00:06.04
    2284 bitrate=8171.4kbits/s speed=3.99x frame= 317 fps=157 q=25.0 size= 12658kB
    2285 time=00:00:09.52 bitrate=10891.7kbits/s speed=4.73x frame= 404 fps=161 q=25.0
    2286 size= 18823kB time=00:00:13.00 bitrate=11861.3kbits/s speed=5.17x frame= 482
    2287 fps=160 q=25.0 size= 24254kB time=00:00:16.12 bitrate=12325.6kbits/s
    2288 speed=5.35x frame= 569 fps=162 q=25.0 size= 30513kB time=00:00:19.60
    2289 bitrate=12753.0kbits/s speed=5.57x frame= 656 fps=162 q=25.0 size= 36817kB
    2290 time=00:00:23.08 bitrate=13067.8kbits/s speed= 5.7x frame= 744 fps=164 q=25.0
    2291 size= 43111kB time=00:00:26.60 bitrate=13276.7kbits/s speed=5.85x frame= 833
    2292 fps=165 q=25.0 size= 49483kB time=00:00:30.16 bitrate=13440.4kbits/s
    2293 speed=5.97x frame= 917 fps=165 q=25.0 size= 55575kB time=00:00:33.52
    2294 bitrate=13582.0kbits/s speed=6.04x frame= 1006 fps=166 q=25.0 size= 61701kB
    2295 time=00:00:37.08 bitrate=13631.5kbits/s speed=6.12x frame= 1091 fps=166 q=25.0
    2296 size= 67214kB time=00:00:40.48 bitrate=13602.1kbits/s speed=6.17x frame= 1180
    2297 fps=167 q=25.0 size= 72771kB time=00:00:44.04 bitrate=13536.4kbits/s
    2298 speed=6.24x frame= 1269 fps=168 q=25.0 size= 78098kB time=00:00:47.60
    2299 bitrate=13440.7kbits/s speed=6.29x frame= 1353 fps=168 q=25.0 size= 82790kB
    2300 time=00:00:50.96 bitrate=13308.7kbits/s speed=6.32x frame= 1442 fps=168 q=25.0
    2301 size= 87426kB time=00:00:54.52 bitrate=13136.4kbits/s speed=6.36x frame= 1532
    2302 fps=169 q=25.0 size= 91864kB time=00:00:58.12 bitrate=12948.3kbits/s speed=
    2303 6.4x frame= 1617 fps=169 q=25.0 size= 95915kB time=00:01:01.52
    2304 bitrate=12772.1kbits/s speed=6.42x frame= 1706 fps=169 q=25.0 size= 99937kB
    2305 time=00:01:05.08 bitrate=12579.7kbits/s speed=6.45x frame= 1795 fps=170 q=25.0
    2306 size= 103922kB time=00:01:08.64 bitrate=12402.8kbits/s speed=6.48x frame= 1878
    2307 fps=169 q=25.0 size= 107590kB time=00:01:11.96 bitrate=12248.1kbits/s
    2308 speed=6.49x frame= 1966 fps=170 q=25.0 size= 110849kB time=00:01:15.48
    2309 bitrate=12030.7kbits/s speed=6.51x frame= 2054 fps=170 q=25.0 size= 116186kB
    2310 time=00:01:19.00 bitrate=12048.1kbits/s speed=6.53x frame= 2142 fps=170 q=25.0
    2311 size= 121307kB time=00:01:22.52 bitrate=12042.5kbits/s speed=6.55x frame= 2230
    2312 fps=170 q=25.0 size= 127266kB time=00:01:26.04 bitrate=12117.2kbits/s
    2313 speed=6.57x frame= 2318 fps=170 q=25.0 size= 131561kB time=00:01:29.56
    2314 bitrate=12033.8kbits/s speed=6.59x frame= 2405 fps=171 q=25.0 size= 134057kB
    2315 time=00:01:33.04 bitrate=11803.4kbits/s speed= 6.6x frame= 2494 fps=171 q=25.0
    2316 size= 135297kB time=00:01:36.60 bitrate=11473.6kbits/s speed=6.62x frame= 2584
    2317 fps=171 q=25.0 size= 136340kB time=00:01:40.20 bitrate=11146.7kbits/s
    2318 speed=6.63x frame= 2667 fps=171 q=25.0 size= 137370kB time=00:01:43.52
    2319 bitrate=10870.7kbits/s speed=6.63x frame= 2749 fps=171 q=25.0 size= 138613kB
    2320 time=00:01:46.80 bitrate=10632.2kbits/s speed=6.63x frame= 2830 fps=170 q=25.0
    2321 size= 139607kB time=00:01:50.04 bitrate=10393.1kbits/s speed=6.62x frame= 2910
    2322 fps=170 q=25.0 size= 140624kB time=00:01:53.24 bitrate=10173.0kbits/s
    2323 speed=6.61x frame= 2994 fps=170 q=25.0 size= 141666kB time=00:01:56.60
    2324 bitrate=9953.0kbits/s speed=6.61x frame= 3078 fps=170 q=25.0 size= 142646kB
    2325 time=00:01:59.96 bitrate=9741.2kbits/s speed=6.62x frame= 3167 fps=170 q=25.0
    2326 size= 143594kB time=00:02:03.52 bitrate=9523.3kbits/s speed=6.63x frame= 3254
    2327 fps=170 q=25.0 size= 144663kB time=00:02:07.00 bitrate=9331.4kbits/s
    2328 speed=6.64x frame= 3345 fps=170 q=25.0 size= 145501kB time=00:02:10.64
    2329 bitrate=9123.9kbits/s speed=6.65x frame= 3436 fps=171 q=25.0 size= 146505kB
    2330 time=00:02:14.28 bitrate=8937.8kbits/s speed=6.67x frame= 3527 fps=171 q=25.0
    2331 size= 147412kB time=00:02:17.92 bitrate=8755.8kbits/s speed=6.68x frame= 3618
    2332 fps=171 q=25.0 size= 148221kB time=00:02:21.56 bitrate=8577.5kbits/s
    2333 speed=6.69x frame= 3709 fps=171 q=25.0 size= 149054kB time=00:02:25.20
    2334 bitrate=8409.4kbits/s speed=6.71x frame= 3800 fps=172 q=25.0 size= 149760kB
    2335 time=00:02:28.84 bitrate=8242.7kbits/s speed=6.72x frame= 3891 fps=172 q=25.0
    2336 size= 150377kB time=00:02:32.48 bitrate=8079.0kbits/s speed=6.73x frame= 3982
    2337 fps=172 q=25.0 size= 151132kB time=00:02:36.12 bitrate=7930.3kbits/s
    2338 speed=6.74x frame= 4029 fps=171 q=-1.0 Lsize= 152060kB time=00:02:41.04
    2339 bitrate=7735.2kbits/s speed=6.85x 
    2340 video:152015kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
    2341 muxing overhead: 0.029385% 
    2342 [libx264 @ 0x2f41260] frame I:18 Avg QP:11.68 size:146649 
    2343 [libx264 @ 0x2f41260] frame P:1617 Avg QP:18.50 size: 44842 
    2344 [libx264 @ 0x2f41260] frame B:2394 Avg QP:23.32 size: 33631 
    2345 [libx264 @ 0x2f41260] consecutive B-frames: 16.9% 7.5% 12.4% 63.1% 
    2346 [libx264 @ 0x2f41260] mb I I16..4: 52.0% 30.2% 17.8% 
    2347 [libx264 @ 0x2f41260] mb P I16..4: 1.1% 3.0% 1.6% P16..4: 7.9% 4.3% 4.4% 0.0%
    2348 0.0% skip:77.7% 
    2349 [libx264 @ 0x2f41260] mb B I16..4: 0.3% 1.2% 0.6% B16..8: 9.2% 3.0% 1.5%
    2350 direct: 5.0% skip:79.1% L0:34.0% L1:38.4% BI:27.6% 
    2351 [libx264 @ 0x2f41260] 8x8 transform intra:51.8% inter:33.7% 
    2352 [libx264 @ 0x2f41260] coded y,uvDC,uvAC intra: 70.6% 35.1% 31.0% inter: 10.9%
    2353 6.3% 4.1% 
    2354 [libx264 @ 0x2f41260] i16 v,h,dc,p: 68% 29% 3% 1% 
    2355 [libx264 @ 0x2f41260] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 6% 39% 7% 7% 9% 5% 8%
    2356 7% 
    2357 [libx264 @ 0x2f41260] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 9% 20% 9% 9% 12% 8%
    2358 10% 8% 
    2359 [libx264 @ 0x2f41260] i8c dc,h,v,p: 70% 13% 16% 2% 
    2360 [libx264 @ 0x2f41260] Weighted P-Frames: Y:0.1% UV:0.1% 
    2361 [libx264 @ 0x2f41260] ref P L0: 72.3% 12.7% 9.9% 5.1% 0.0% 
    2362 [libx264 @ 0x2f41260] ref B L0: 89.2% 8.1% 2.6% 
    2363 [libx264 @ 0x2f41260] ref B L1: 97.6% 2.4% 
    2364 [libx264 @ 0x2f41260] kb/s:7727.11 
    2365  
    2366 Movie saved to /tmp/imprima/.../movies/F107-A3_full_bin2_srv.mp4 
    2367  
    2368 executed F107-A3_session.cxc 
    2369 
    2370 > close session
    2371 
    2372 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    2373 
    2374 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2375 step 1, values int8 
    2376 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2377 shown at step 1, values int8 
    2378 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2379 shown at step 1, values int8 
    2380 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2381 shown at step 1, values int8 
    2382 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2383 shown at step 1, values int8 
    2384 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    2385 © 2016-2022 Regents of the University of California. All rights reserved. 
    2386 How to cite UCSF ChimeraX 
    2387 
    2388 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2389 
    2390 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2391 step 2, values int8 
    2392 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2393 shown at level 0.8, step 2, values int8 
    2394 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2395 shown at level 0.8, step 3, values int8 
    2396 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2397 shown at level 0.8, step 2, values int8 
    2398 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2399 shown at level 0.8, step 2, values int8 
    2400 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    2401 the model panel to edit those fields 
    2402 UCSF ChimeraX version: 1.4 (2022-06-03) 
    2403 © 2016-2022 Regents of the University of California. All rights reserved. 
    2404 How to cite UCSF ChimeraX 
    2405 
    2406 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    2407 
    2408 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2409 step 1, values int8 
    2410 
    2411 > volume showOutlineBox true
    2412 
    2413 > volume region all imageMode "full region"
    2414 
    2415 > volume unzone
    2416 
    2417 > mousemode rightMode "crop volume"
    2418 
    2419 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    2420 > "box faces"
    2421 
    2422 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2423 
    2424 > volume #1 region 0,0,0,1385,1409,1604
    2425 
    2426 > volume #1 region all
    2427 
    2428 > volume #1 region 0,0,0,2129,1523,1748
    2429 
    2430 > view orient
    2431 
    2432 > zoom 0.85
    2433 
    2434 > view name p1
    2435 
    2436 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2437 
    2438 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2439 shown at step 1, values int8 
    2440 
    2441 > close #2
    2442 
    2443 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    2444 
    2445 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2446 shown at step 1, values int8 
    2447 
    2448 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    2449 
    2450 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2451 shown at step 1, values int8 
    2452 
    2453 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2454 
    2455 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2456 shown at step 1, values int8 
    2457 
    2458 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    2459 
    2460 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2461 shown at step 1, values int8 
    2462 
    2463 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2464 
    2465 > volume #2 show style surface level 0.8 color #5555ff
    2466 
    2467 > volume #1 region 0,0,0,2129,1523,1740
    2468 
    2469 > volume all region 0,0,0,2129,1523,1740
    2470 
    2471 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2472 > showOutlineBox true imageMode "box faces"
    2473 
    2474 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2475 > showOutlineBox true imageMode "box faces"
    2476 
    2477 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2478 > showOutlineBox true imageMode "box faces"
    2479 
    2480 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    2481 > faces"
    2482 
    2483 > volume #2 show style surface level -50 color #5555ff
    2484 
    2485 > volume #2 show style surface level 10 color #5555ff
    2486 
    2487 > lighting soft
    2488 
    2489 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2490 
    2491 > volume #2 show style surface level 0.8 color #5555ff
    2492 
    2493 > volume #3 show style surface level 0.8 color #aa557f
    2494 
    2495 > volume #4 show style surface level 0.8 color #f514fd
    2496 
    2497 > volume #5 show style surface level 0.8 color #11ffcc
    2498 
    2499 > ~display #1
    2500 
    2501 > volume #2 transparency 0.6
    2502 
    2503 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2504 
    2505 > display #1
    2506 
    2507 > volume all region 0,0,0,2129,1523,1744
    2508 
    2509 > ~display #1
    2510 
    2511 > volume #2 show style surface step 2
    2512 
    2513 > volume #3 show style surface step 3
    2514 
    2515 > volume #4 show style surface step 2
    2516 
    2517 > volume #5 show style surface step 2
    2518 
    2519 > volume #5 show style surface step 1
    2520 
    2521 > volume #5 show style surface step 2
    2522 
    2523 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2524 
    2525 > view name p2
    2526 
    2527 > view list
    2528 
    2529 Named views: p1, p2 
    2530 
    2531 > view p1
    2532 
    2533 > view p2
    2534 
    2535 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2536 
    2537 > fly p2 p1 100
    2538 
    2539 > wait
    2540 
    2541 > view p2
    2542 
    2543 > display #1
    2544 
    2545 > volume #1 region 0,0,0,2129,1523,1744
    2546 
    2547 > volume #1 region 0,0,0,2129,1523,1740
    2548 
    2549 > volume #1 region 0,0,0,2129,1523,1742
    2550 
    2551 > volume #1 region 0,0,0,2129,1523,1743
    2552 
    2553 > volume #1 region 0,0,0,2129,1523,1744
    2554 
    2555 > volume #1 region 0,0,0,2129,1523,1743
    2556 
    2557 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2558 
    2559 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    2560 
    2561 opened ChimeraX session 
    2562 
    2563 > display #1
    2564 
    2565 > ~display #2-5
    2566 
    2567 > display #2-5
    2568 
    2569 > ~display #1
    2570 
    2571 > display #1
    2572 
    2573 > ~display #2-5
    2574 
    2575 > volume all region 0,0,0,2129,1523,1743
    2576 
    2577 > display #2-5
    2578 
    2579 > view p2
    2580 
    2581 > lighting soft
    2582 
    2583 > view p1
    2584 
    2585 > help hide
    2586 
    2587 > hide #1
    2588 
    2589 > view p2
    2590 
    2591 > show #2
    2592 
    2593 > volume #2-5 show style surface
    2594 
    2595 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2596 
    2597 > display #1
    2598 
    2599 > ~display #2-5
    2600 
    2601 > volume #2-5 show style surface
    2602 
    2603 > ~display #2-5
    2604 
    2605 > fly p2 p1 100
    2606 
    2607 > wait
    2608 
    2609 > volume #2-5 show style surface transparency 0.5
    2610 
    2611 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    2612 > bgColor black margin 5
    2613 
    2614 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    2615 > bgColor black margin 5
    2616 
    2617 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    2618 > true bgColor black margin 5
    2619 
    2620 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    2621 > true bgColor black margin 5
    2622 
    2623 > volume all planes z,1743,30
    2624 
    2625 > wait 1700
    2626 
    2627 > close session
    2628 
    2629 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    2630 
    2631 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2632 step 1, values int8 
    2633 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2634 shown at level 0.8, step 1, values int8 
    2635 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2636 shown at level 0.8, step 1, values int8 
    2637 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2638 shown at level 0.8, step 1, values int8 
    2639 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2640 shown at level 0.8, step 1, values int8 
    2641 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    2642 © 2016-2022 Regents of the University of California. All rights reserved. 
    2643 How to cite UCSF ChimeraX 
    2644 
    2645 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2646 
    2647 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2648 step 2, values int8 
    2649 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2650 shown at level 0.8, step 2, values int8 
    2651 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2652 shown at level 0.8, step 3, values int8 
    2653 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2654 shown at level 0.8, step 2, values int8 
    2655 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2656 shown at level 0.8, step 2, values int8 
    2657 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    2658 the model panel to edit those fields 
    2659 UCSF ChimeraX version: 1.4 (2022-06-03) 
    2660 © 2016-2022 Regents of the University of California. All rights reserved. 
    2661 How to cite UCSF ChimeraX 
    2662 
    2663 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    2664 
    2665 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    2666 step 1, values int8 
    2667 
    2668 > volume showOutlineBox true
    2669 
    2670 > volume region all imageMode "full region"
    2671 
    2672 > volume unzone
    2673 
    2674 > mousemode rightMode "crop volume"
    2675 
    2676 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    2677 > "box faces"
    2678 
    2679 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2680 
    2681 > volume #1 region 0,0,0,1385,1409,1604
    2682 
    2683 > volume #1 region all
    2684 
    2685 > volume #1 region 0,0,0,2129,1523,1748
    2686 
    2687 > view orient
    2688 
    2689 > zoom 0.85
    2690 
    2691 > view name p1
    2692 
    2693 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2694 
    2695 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2696 shown at step 1, values int8 
    2697 
    2698 > close #2
    2699 
    2700 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    2701 
    2702 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    2703 shown at step 1, values int8 
    2704 
    2705 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    2706 
    2707 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    2708 shown at step 1, values int8 
    2709 
    2710 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    2711 
    2712 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    2713 shown at step 1, values int8 
    2714 
    2715 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    2716 
    2717 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    2718 shown at step 1, values int8 
    2719 
    2720 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2721 
    2722 > volume #2 show style surface level 0.8 color #5555ff
    2723 
    2724 > volume #1 region 0,0,0,2129,1523,1740
    2725 
    2726 > volume all region 0,0,0,2129,1523,1740
    2727 
    2728 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2729 > showOutlineBox true imageMode "box faces"
    2730 
    2731 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2732 > showOutlineBox true imageMode "box faces"
    2733 
    2734 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    2735 > showOutlineBox true imageMode "box faces"
    2736 
    2737 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    2738 > faces"
    2739 
    2740 > volume #2 show style surface level -50 color #5555ff
    2741 
    2742 > volume #2 show style surface level 10 color #5555ff
    2743 
    2744 > lighting soft
    2745 
    2746 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2747 
    2748 > volume #2 show style surface level 0.8 color #5555ff
    2749 
    2750 > volume #3 show style surface level 0.8 color #aa557f
    2751 
    2752 > volume #4 show style surface level 0.8 color #f514fd
    2753 
    2754 > volume #5 show style surface level 0.8 color #11ffcc
    2755 
    2756 > ~display #1
    2757 
    2758 > volume #2 transparency 0.6
    2759 
    2760 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2761 
    2762 > display #1
    2763 
    2764 > volume all region 0,0,0,2129,1523,1744
    2765 
    2766 > ~display #1
    2767 
    2768 > volume #2 show style surface step 2
    2769 
    2770 > volume #3 show style surface step 3
    2771 
    2772 > volume #4 show style surface step 2
    2773 
    2774 > volume #5 show style surface step 2
    2775 
    2776 > volume #5 show style surface step 1
    2777 
    2778 > volume #5 show style surface step 2
    2779 
    2780 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2781 
    2782 > view name p2
    2783 
    2784 > view list
    2785 
    2786 Named views: p1, p2 
    2787 
    2788 > view p1
    2789 
    2790 > view p2
    2791 
    2792 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2793 
    2794 > fly p2 p1 100
    2795 
    2796 > wait
    2797 
    2798 > view p2
    2799 
    2800 > display #1
    2801 
    2802 > volume #1 region 0,0,0,2129,1523,1744
    2803 
    2804 > volume #1 region 0,0,0,2129,1523,1740
    2805 
    2806 > volume #1 region 0,0,0,2129,1523,1742
    2807 
    2808 > volume #1 region 0,0,0,2129,1523,1743
    2809 
    2810 > volume #1 region 0,0,0,2129,1523,1744
    2811 
    2812 > volume #1 region 0,0,0,2129,1523,1743
    2813 
    2814 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2815 
    2816 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    2817 
    2818 opened ChimeraX session 
    2819 
    2820 > display #1
    2821 
    2822 > ~display #2-5
    2823 
    2824 > display #2-5
    2825 
    2826 > ~display #1
    2827 
    2828 > display #1
    2829 
    2830 > ~display #2-5
    2831 
    2832 > volume all region 0,0,0,2129,1523,1743
    2833 
    2834 > display #2-5
    2835 
    2836 > view p2
    2837 
    2838 > lighting soft
    2839 
    2840 > view p1
    2841 
    2842 > help hide
    2843 
    2844 > hide #1
    2845 
    2846 > view p2
    2847 
    2848 > show #2
    2849 
    2850 > volume #2-5 show style surface
    2851 
    2852 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2853 
    2854 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    2855 
    2856 opened ChimeraX session 
    2857 
    2858 > display #1
    2859 
    2860 > ~display #2-5
    2861 
    2862 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    2863 
    2864 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    2865 
    2866 opened ChimeraX session 
    2867 
    2868 > view orient
    2869 
    2870 > close session
    2871 
    2872 > open /tmp/imprima/F107A1_bin2/data/f107a_flipz.mrc
    2873 
    2874 Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
    2875 step 1, values int8 
    2876 
    2877 > save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
    2878 
    2879 > volume showOutlineBox true
    2880 
    2881 > volume #1 region 0,0,0,1646,1505,1349 step 8
    2882 
    2883 > volume #1 region 0,0,0,1646,1505,1349 step 1 colorMode opaque8 imageMode
    2884 > "box faces"
    2885 
    2886 > view orient
    2887 
    2888 > view name p1
    2889 
    2890 > view list
    2891 
    2892 Named views: p1 
    2893 
    2894 > save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
    2895 
    2896 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    2897 
    2898 > view name p2
    2899 
    2900 > ui mousemode right "crop volume"
    2901 
    2902 > volume #1 region 0,0,0,1646,1505,1094
    2903 
    2904 > view p1
    2905 
    2906 > volume #1 region 0,0,0,1646,1505,1349
    2907 
    2908 > volume #1 planes z,1349,1094
    2909 
    2910 > wait 255
    2911 
    2912 > wait
    2913 
    2914 wait requires a frame count argument unless motion is in progress 
    2915 
    2916 > volume #1 region 0,0,0,1646,1505,1349
    2917 
    2918 > volume #1 planes z,1349,1094
    2919 
    2920 > wait 255
    2921 
    2922 > volume #1 region 0,0,0,1646,1505,1349
    2923 
    2924 > volume #1 planes z,1349,1300
    2925 
    2926 > wait 50
    2927 
    2928 > help 2dlabels
    2929 
    2930 [Repeated 1 time(s)]
    2931 
    2932 > volume #1 region 0,0,0,1646,1505,1349
    2933 
    2934 > volume #1 planes z,1349,1300
    2935 
    2936 > wait 50
    2937 
    2938 > volume #1 region 0,0,0,1646,1505,1349
    2939 
    2940 > 2dlabels arrow #7.1 start 0.083,0.643 end 0.357,0.413 color red weight 0.7
    2941 > headStyle solid
    2942 
    2943 No 2D arrows in session 
    2944 
    2945 > 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.7
    2946 > headStyle solid
    2947 
    2948 > volume #1 region 0,0,0,1646,1505,1349
    2949 
    2950 > view p1
    2951 
    2952 > ui mousemode right "move label"
    2953 
    2954 > 2dlabels arrow #2.1 end 0.363,0.765
    2955 
    2956 > 2dlabels arrow #2.1 start 0.112,0.919
    2957 
    2958 > 2dlabels arrow #2.1 start 0.112,0.919 end 0.363,0.765 color white
    2959 
    2960 > 2dlabels arrow start 0.112,0.819 end 0.363,0.765 color white
    2961 
    2962 > 2dlabels arrow #2.1 end 0.362,0.785
    2963 
    2964 > 2dlabels arrow #2.2 end 0.343,0.523
    2965 
    2966 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white
    2967 
    2968 > help 2dlabels
    2969 
    2970 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white bold false
    2971 
    2972 Expected a keyword 
    2973 
    2974 > help 2dlabels
    2975 
    2976 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 bold false color white
    2977 
    2978 Expected ',' or a keyword 
    2979 
    2980 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white, bold
    2981 > false
    2982 
    2983 Invalid "color" argument: Expected 'default' or a color 
    2984 
    2985 > view p1
    2986 
    2987 > help 2dlabels
    2988 
    2989 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white weight 0.5
    2990 
    2991 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    2992 > margin 5 visibility true
    2993 
    2994 > 2dlabels arrow #2.1 weight 0.5
    2995 
    2996 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    2997 
    2998 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    2999 > margin 5 visibility true
    3000 
    3001 > 2dlabels arrow #2.1 end 0.362,0.784
    3002 
    3003 > 2dlabels arrow #2.1 start 0.112,0.916
    3004 
    3005 > 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.5
    3006 > headStyle solid
    3007 
    3008 > 2dlabels arrow #2.3 start 0.830,0.911
    3009 
    3010 > 2dlabels arrow #2.3 end 0.580,0.728
    3011 
    3012 > 2dlabels arrow #2.3 start 0.824,0.922
    3013 
    3014 > 2dlabels arrow #2.3 start 0.824,0.922 end 0.580,0.728 color white
    3015 
    3016 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    3017 
    3018 > 2dlabels arrow start 0.824,0.922 end 0.780,0.928 color white
    3019 
    3020 > 2dlabels arrow #2.4 end 0.652,0.427
    3021 
    3022 > 2dlabels arrow #2.3 start 0.813,0.939
    3023 
    3024 > 2dlabels arrow #2.4 start 0.851,0.886
    3025 
    3026 > 2dlabels arrow #2.4 weight 0.5
    3027 
    3028 > 2dlabels arrow #2.4 weight 0.5 headStyle solid
    3029 
    3030 > 2dlabels arrow #2.4 end 0.655,0.424
    3031 
    3032 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    3033 
    3034 > volume #1 region 0,0,0,1646,1505,1349
    3035 
    3036 [Repeated 1 time(s)]
    3037 
    3038 > volume #1 region 0,0,0,1646,1505,1300
    3039 
    3040 > 2dlabels arrow #2.1 end 0.442,0.807
    3041 
    3042 > 2dlabels arrow #2.2 end 0.331,0.561
    3043 
    3044 > 2dlabels arrow #2.3 end 0.591,0.756
    3045 
    3046 > 2dlabels arrow #2.4 end 0.662,0.510
    3047 
    3048 > volume #1 region 0,0,0,1646,1505,1349
    3049 
    3050 > help 2dlabels\
    3051 
    3052 No help found for '2dlabels\' 
    3053 
    3054 > help 2dlabels
    3055 
    3056 > 2dlabels #all visbility false
    3057 
    3058 Expected 'all' or a 2d label name or a label models specifier or a keyword 
    3059 
    3060 > 2dlabels all visbility false
    3061 
    3062 Expected a keyword 
    3063 
    3064 > 2dlabels all visibility false
    3065 
    3066 > 2dlabels arrow all visibility false
    3067 
    3068 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    3069 
    3070 > volume #1 region 0,0,0,1646,1505,1300
    3071 
    3072 > volume #1 region 0,0,0,1646,1300,1000 wait 100;
    3073 
    3074 Expected a keyword 
    3075 
    3076 > volume #1 region 0,0,0,1646,1300,1000
    3077 
    3078 > wait 100
    3079 
    3080 > volume #1 region 0,0,0,1646,1505,1349
    3081 
    3082 > volume #1 planes z,1349,1300
    3083 
    3084 > wait 50
    3085 
    3086 > volume #1 planes z,1300,1000
    3087 
    3088 > wait 101
    3089 
    3090 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    3091 
    3092 > volume #1 region 0,0,0,1646,1505,1349
    3093 
    3094 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    3095 
    3096 ——— End of log from Fri Jul 29 13:26:07 2022 ———
    3097 
    3098 opened ChimeraX session 
    3099 
    3100 > close #2
    3101 
    3102 > close #3
    3103 
    3104 > ui mousemode right "crop volume"
    3105 
    3106 > volume #1 region 0,0,0,1646,1505,1349
    3107 
    3108 > ui mousemode right "move label"
    3109 
    3110 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations_base.cxc
    3111 
    3112 > movie record supersample 3
    3113 
    3114 > volume #1 planes z,1349,30
    3115 
    3116 > wait 1320
    3117 
    3118 > movie encode framerate 25 quality highest output
    3119 > /tmp/imprima/F107A1_bin2/movies/F107-A1_fly-base_srv.mp4 verbose true format
    3120 > h264
    3121 
    3122 /usr/libexec/UCSF-ChimeraX/bin/ffmpeg -r 25.0 -i /tmp/chimovie_Z9K5-%05d.ppm
    3123 -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4
    3124 -pix_fmt yuv420p -crf 15 /tmp/imprima/F107A1_bin2/movies/F107-A1_fly-
    3125 base_srv.mp4 
    3126 stdout: 
    3127  
    3128 stderr: 
    3129 ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers 
    3130 built with gcc 8 (GCC) 
    3131 configuration: --prefix=/tmp/chx-v1.4.jOWCxR/build --enable-gpl --enable-
    3132 version3 --disable-network --disable-doc --disable-devices --disable-ffplay
    3133 --disable-ffserver --disable-ffprobe --enable-libtheora --enable-libvpx
    3134 --enable-libx264 --yasmexe=/tmp/chx-v1.4.jOWCxR/build/bin/yasm --optflags=-O
    3135 --extra-cflags=-I/tmp/chx-v1.4.jOWCxR/build/include --extra-ldflags='-O3 -Wall
    3136 -Wextra -D_FORTIFY=2 -L/tmp/chx-v1.4.jOWCxR/build/lib' --extra-libs=-ldl 
    3137 libavutil 55. 34.101 / 55. 34.101 
    3138 libavcodec 57. 64.101 / 57. 64.101 
    3139 libavformat 57. 56.101 / 57. 56.101 
    3140 libavdevice 57. 1.100 / 57. 1.100 
    3141 libavfilter 6. 65.100 / 6. 65.100 
    3142 libswscale 4. 2.100 / 4. 2.100 
    3143 libswresample 2. 3.100 / 2. 3.100 
    3144 libpostproc 54. 1.100 / 54. 1.100 
    3145 Input #0, image2, from '/tmp/chimovie_Z9K5-%05d.ppm': 
    3146 Duration: 00:00:52.80, start: 0.000000, bitrate: N/A 
    3147 Stream #0:0: Video: ppm, rgb24, 1308x1033, 25 tbr, 25 tbn, 25 tbc 
    3148 [libx264 @ 0x3723180] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
    3149 FMA3 AVX2 LZCNT BMI2 
    3150 [libx264 @ 0x3723180] profile High, level 4.0 
    3151 [libx264 @ 0x3723180] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
    3152 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
    3153 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
    3154 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
    3155 fast_pskip=1 chroma_qp_offset=-2 threads=32 lookahead_threads=5
    3156 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
    3157 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
    3158 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
    3159 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=15.0 qcomp=0.60 qpmin=0
    3160 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 
    3161 Output #0, mp4, to '/tmp/imprima/F107A1_bin2/movies/F107-A1_fly-base_srv.mp4': 
    3162 Metadata: 
    3163 encoder : Lavf57.56.101 
    3164 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
    3165 1308x1032, q=-1--1, 25 fps, 12800 tbn, 25 tbc 
    3166 Metadata: 
    3167 encoder : Lavc57.64.101 libx264 
    3168 Side data: 
    3169 cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 
    3170 Stream mapping: 
    3171 Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) 
    3172 Press [q] to stop, [?] for help 
    3173 frame= 95 fps=0.0 q=20.0 size= 1636kB time=00:00:00.64 bitrate=20943.5kbits/s
    3174 speed=1.27x frame= 200 fps=198 q=20.0 size= 10651kB time=00:00:04.84
    3175 bitrate=18027.9kbits/s speed= 4.8x frame= 309 fps=204 q=20.0 size= 20788kB
    3176 time=00:00:09.20 bitrate=18510.2kbits/s speed=6.08x frame= 423 fps=210 q=20.0
    3177 size= 32797kB time=00:00:13.76 bitrate=19525.4kbits/s speed=6.83x frame= 533
    3178 fps=212 q=20.0 size= 44524kB time=00:00:18.16 bitrate=20084.7kbits/s
    3179 speed=7.21x frame= 649 fps=215 q=20.0 size= 56472kB time=00:00:22.80
    3180 bitrate=20290.4kbits/s speed=7.55x frame= 761 fps=216 q=20.0 size= 67928kB
    3181 time=00:00:27.28 bitrate=20398.4kbits/s speed=7.75x frame= 876 fps=218 q=20.0
    3182 size= 79048kB time=00:00:31.88 bitrate=20312.4kbits/s speed=7.92x frame= 991
    3183 fps=219 q=20.0 size= 89745kB time=00:00:36.48 bitrate=20153.1kbits/s
    3184 speed=8.06x frame= 1107 fps=220 q=20.0 size= 100107kB time=00:00:41.12
    3185 bitrate=19943.4kbits/s speed=8.18x frame= 1219 fps=220 q=20.0 size= 109582kB
    3186 time=00:00:45.60 bitrate=19686.3kbits/s speed=8.25x frame= 1320 fps=216 q=-1.0
    3187 Lsize= 120621kB time=00:00:52.68 bitrate=18757.1kbits/s speed=8.64x 
    3188 video:120604kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
    3189 muxing overhead: 0.014401% 
    3190 [libx264 @ 0x3723180] frame I:6 Avg QP: 9.40 size:141615 
    3191 [libx264 @ 0x3723180] frame P:332 Avg QP:16.19 size:123505 
    3192 [libx264 @ 0x3723180] frame B:982 Avg QP:19.71 size: 83140 
    3193 [libx264 @ 0x3723180] consecutive B-frames: 0.6% 0.3% 0.9% 98.2% 
    3194 [libx264 @ 0x3723180] mb I I16..4: 50.1% 32.1% 17.8% 
    3195 [libx264 @ 0x3723180] mb P I16..4: 2.6% 8.5% 15.7% P16..4: 0.8% 0.9% 0.6% 0.0%
    3196 0.0% skip:70.9% 
    3197 [libx264 @ 0x3723180] mb B I16..4: 0.3% 1.0% 2.6% B16..8: 6.0% 2.0% 1.8%
    3198 direct:14.5% skip:71.9% L0:29.5% L1:25.1% BI:45.5% 
    3199 [libx264 @ 0x3723180] 8x8 transform intra:30.0% inter:36.5% 
    3200 [libx264 @ 0x3723180] coded y,uvDC,uvAC intra: 86.5% 0.0% 0.0% inter: 18.2%
    3201 0.0% 0.0% 
    3202 [libx264 @ 0x3723180] i16 v,h,dc,p: 64% 35% 1% 0% 
    3203 [libx264 @ 0x3723180] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 8% 28% 7% 10% 9% 9%
    3204 8% 9% 
    3205 [libx264 @ 0x3723180] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 9% 18% 9% 11% 11% 11%
    3206 10% 11% 
    3207 [libx264 @ 0x3723180] i8c dc,h,v,p: 100% 0% 0% 0% 
    3208 [libx264 @ 0x3723180] Weighted P-Frames: Y:28.6% UV:0.0% 
    3209 [libx264 @ 0x3723180] ref P L0: 50.9% 13.9% 19.0% 12.9% 3.2% 
    3210 [libx264 @ 0x3723180] ref B L0: 93.9% 4.2% 1.9% 
    3211 [libx264 @ 0x3723180] ref B L1: 99.5% 0.5% 
    3212 [libx264 @ 0x3723180] kb/s:18711.71 
    3213  
    3214 Movie saved to /tmp/imprima/.../movies/F107-A1_fly-base_srv.mp4 
    3215  
    3216 executed chimerax_flythrough_annotations_base.cxc 
    3217 
    3218 > volume #1 region 0,0,0,1646,1505,1349
    3219 
    3220 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations_base.cxc
    3221 
    3222 > movie record supersample 3
    3223 
    3224 > volume #1 planes z,1349,30
    3225 
    3226 > wait 1320
    3227 
    3228 > movie encode framerate 25 quality highest output
    3229 > /tmp/imprima/F107A1_bin2/movies/F107-A1_fly-base_srv.mp4 verbose true format
    3230 > h264
    3231 
    3232 /usr/libexec/UCSF-ChimeraX/bin/ffmpeg -r 25.0 -i /tmp/chimovie_w6Yc-%05d.ppm
    3233 -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4
    3234 -pix_fmt yuv420p -crf 15 /tmp/imprima/F107A1_bin2/movies/F107-A1_fly-
    3235 base_srv.mp4 
    3236 stdout: 
    3237  
    3238 stderr: 
    3239 ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers 
    3240 built with gcc 8 (GCC) 
    3241 configuration: --prefix=/tmp/chx-v1.4.jOWCxR/build --enable-gpl --enable-
    3242 version3 --disable-network --disable-doc --disable-devices --disable-ffplay
    3243 --disable-ffserver --disable-ffprobe --enable-libtheora --enable-libvpx
    3244 --enable-libx264 --yasmexe=/tmp/chx-v1.4.jOWCxR/build/bin/yasm --optflags=-O
    3245 --extra-cflags=-I/tmp/chx-v1.4.jOWCxR/build/include --extra-ldflags='-O3 -Wall
    3246 -Wextra -D_FORTIFY=2 -L/tmp/chx-v1.4.jOWCxR/build/lib' --extra-libs=-ldl 
    3247 libavutil 55. 34.101 / 55. 34.101 
    3248 libavcodec 57. 64.101 / 57. 64.101 
    3249 libavformat 57. 56.101 / 57. 56.101 
    3250 libavdevice 57. 1.100 / 57. 1.100 
    3251 libavfilter 6. 65.100 / 6. 65.100 
    3252 libswscale 4. 2.100 / 4. 2.100 
    3253 libswresample 2. 3.100 / 2. 3.100 
    3254 libpostproc 54. 1.100 / 54. 1.100 
    3255 Input #0, image2, from '/tmp/chimovie_w6Yc-%05d.ppm': 
    3256 Duration: 00:00:52.80, start: 0.000000, bitrate: N/A 
    3257 Stream #0:0: Video: ppm, rgb24, 1308x1033, 25 tbr, 25 tbn, 25 tbc 
    3258 [libx264 @ 0x3b38180] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
    3259 FMA3 AVX2 LZCNT BMI2 
    3260 [libx264 @ 0x3b38180] profile High, level 4.0 
    3261 [libx264 @ 0x3b38180] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
    3262 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
    3263 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
    3264 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
    3265 fast_pskip=1 chroma_qp_offset=-2 threads=32 lookahead_threads=5
    3266 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
    3267 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
    3268 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
    3269 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=15.0 qcomp=0.60 qpmin=0
    3270 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 
    3271 Output #0, mp4, to '/tmp/imprima/F107A1_bin2/movies/F107-A1_fly-base_srv.mp4': 
    3272 Metadata: 
    3273 encoder : Lavf57.56.101 
    3274 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
    3275 1308x1032, q=-1--1, 25 fps, 12800 tbn, 25 tbc 
    3276 Metadata: 
    3277 encoder : Lavc57.64.101 libx264 
    3278 Side data: 
    3279 cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 
    3280 Stream mapping: 
    3281 Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) 
    3282 Press [q] to stop, [?] for help 
    3283 frame= 88 fps=0.0 q=20.0 size= 1664kB time=00:00:00.36 bitrate=37861.7kbits/s
    3284 speed=0.71x frame= 188 fps=186 q=20.0 size= 15544kB time=00:00:04.36
    3285 bitrate=29204.8kbits/s speed=4.32x frame= 291 fps=193 q=20.0 size= 30808kB
    3286 time=00:00:08.48 bitrate=29761.6kbits/s speed=5.61x frame= 388 fps=193 q=20.0
    3287 size= 46607kB time=00:00:12.36 bitrate=30890.2kbits/s speed=6.15x frame= 493
    3288 fps=196 q=20.0 size= 64492kB time=00:00:16.56 bitrate=31903.2kbits/s
    3289 speed=6.59x frame= 602 fps=200 q=20.0 size= 82220kB time=00:00:20.92
    3290 bitrate=32196.2kbits/s speed=6.94x frame= 702 fps=200 q=20.0 size= 98714kB
    3291 time=00:00:24.92 bitrate=32450.2kbits/s speed=7.09x frame= 814 fps=203 q=20.0
    3292 size= 116262kB time=00:00:29.40 bitrate=32395.2kbits/s speed=7.31x frame= 920
    3293 fps=203 q=20.0 size= 132389kB time=00:00:33.64 bitrate=32239.2kbits/s
    3294 speed=7.44x frame= 1027 fps=204 q=20.0 size= 147825kB time=00:00:37.92
    3295 bitrate=31935.1kbits/s speed=7.55x frame= 1128 fps=204 q=20.0 size= 162038kB
    3296 time=00:00:41.96 bitrate=31635.3kbits/s speed=7.59x frame= 1233 fps=205 q=20.0
    3297 size= 175734kB time=00:00:46.16 bitrate=31187.4kbits/s speed=7.66x frame= 1320
    3298 fps=200 q=-1.0 Lsize= 191064kB time=00:00:52.68 bitrate=29711.3kbits/s
    3299 speed=7.97x 
    3300 video:191046kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
    3301 muxing overhead: 0.009324% 
    3302 [libx264 @ 0x3b38180] frame I:7 Avg QP:11.37 size:214239 
    3303 [libx264 @ 0x3b38180] frame P:333 Avg QP:18.18 size:189373 
    3304 [libx264 @ 0x3b38180] frame B:980 Avg QP:21.20 size:133744 
    3305 [libx264 @ 0x3b38180] consecutive B-frames: 0.9% 0.0% 0.9% 98.2% 
    3306 [libx264 @ 0x3b38180] mb I I16..4: 40.6% 35.0% 24.4% 
    3307 [libx264 @ 0x3b38180] mb P I16..4: 4.1% 18.1% 21.7% P16..4: 1.2% 1.2% 0.9%
    3308 0.0% 0.0% skip:52.6% 
    3309 [libx264 @ 0x3b38180] mb B I16..4: 0.5% 2.4% 5.0% B16..8: 11.0% 3.7% 3.0%
    3310 direct:20.5% skip:53.8% L0:26.1% L1:22.2% BI:51.7% 
    3311 [libx264 @ 0x3b38180] 8x8 transform intra:37.2% inter:44.7% 
    3312 [libx264 @ 0x3b38180] coded y,uvDC,uvAC intra: 88.8% 0.0% 0.0% inter: 31.2%
    3313 0.0% 0.0% 
    3314 [libx264 @ 0x3b38180] i16 v,h,dc,p: 59% 40% 1% 0% 
    3315 [libx264 @ 0x3b38180] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 8% 26% 8% 11% 10% 9%
    3316 9% 10% 
    3317 [libx264 @ 0x3b38180] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 11% 10% 16% 9% 12% 11%
    3318 10% 10% 11% 
    3319 [libx264 @ 0x3b38180] i8c dc,h,v,p: 100% 0% 0% 0% 
    3320 [libx264 @ 0x3b38180] Weighted P-Frames: Y:23.1% UV:0.0% 
    3321 [libx264 @ 0x3b38180] ref P L0: 46.6% 13.6% 18.0% 18.2% 3.7% 
    3322 [libx264 @ 0x3b38180] ref B L0: 94.4% 3.5% 2.1% 
    3323 [libx264 @ 0x3b38180] ref B L1: 99.6% 0.4% 
    3324 [libx264 @ 0x3b38180] kb/s:29640.94 
    3325  
    3326 Movie saved to /tmp/imprima/.../movies/F107-A1_fly-base_srv.mp4 
    3327  
    3328 executed chimerax_flythrough_annotations_base.cxc 
    3329 
    3330 > volume #1 region 0,0,0,1646,1505,1349
    3331 
    3332 > close session
    3333 
    3334 > open /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs format session
    3335 
    3336 Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
    3337 step 1, values int8 
    3338 Log from Fri Jul 29 13:26:07 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    3339 © 2016-2022 Regents of the University of California. All rights reserved. 
    3340 How to cite UCSF ChimeraX 
    3341 
    3342 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3343 
    3344 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3345 step 1, values int8 
    3346 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3347 shown at step 1, values int8 
    3348 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3349 shown at step 1, values int8 
    3350 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3351 shown at step 1, values int8 
    3352 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3353 shown at step 1, values int8 
    3354 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    3355 © 2016-2022 Regents of the University of California. All rights reserved. 
    3356 How to cite UCSF ChimeraX 
    3357 
    3358 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3359 
    3360 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3361 step 2, values int8 
    3362 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3363 shown at level 0.8, step 2, values int8 
    3364 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3365 shown at level 0.8, step 3, values int8 
    3366 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3367 shown at level 0.8, step 2, values int8 
    3368 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3369 shown at level 0.8, step 2, values int8 
    3370 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    3371 the model panel to edit those fields 
    3372 UCSF ChimeraX version: 1.4 (2022-06-03) 
    3373 © 2016-2022 Regents of the University of California. All rights reserved. 
    3374 How to cite UCSF ChimeraX 
    3375 
    3376 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    3377 
    3378 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3379 step 1, values int8 
    3380 
    3381 > volume showOutlineBox true
    3382 
    3383 > volume region all imageMode "full region"
    3384 
    3385 > volume unzone
    3386 
    3387 > mousemode rightMode "crop volume"
    3388 
    3389 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    3390 > "box faces"
    3391 
    3392 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3393 
    3394 > volume #1 region 0,0,0,1385,1409,1604
    3395 
    3396 > volume #1 region all
    3397 
    3398 > volume #1 region 0,0,0,2129,1523,1748
    3399 
    3400 > view orient
    3401 
    3402 > zoom 0.85
    3403 
    3404 > view name p1
    3405 
    3406 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3407 
    3408 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3409 shown at step 1, values int8 
    3410 
    3411 > close #2
    3412 
    3413 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    3414 
    3415 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3416 shown at step 1, values int8 
    3417 
    3418 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    3419 
    3420 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3421 shown at step 1, values int8 
    3422 
    3423 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3424 
    3425 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3426 shown at step 1, values int8 
    3427 
    3428 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    3429 
    3430 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3431 shown at step 1, values int8 
    3432 
    3433 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3434 
    3435 > volume #2 show style surface level 0.8 color #5555ff
    3436 
    3437 > volume #1 region 0,0,0,2129,1523,1740
    3438 
    3439 > volume all region 0,0,0,2129,1523,1740
    3440 
    3441 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3442 > showOutlineBox true imageMode "box faces"
    3443 
    3444 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3445 > showOutlineBox true imageMode "box faces"
    3446 
    3447 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3448 > showOutlineBox true imageMode "box faces"
    3449 
    3450 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    3451 > faces"
    3452 
    3453 > volume #2 show style surface level -50 color #5555ff
    3454 
    3455 > volume #2 show style surface level 10 color #5555ff
    3456 
    3457 > lighting soft
    3458 
    3459 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3460 
    3461 > volume #2 show style surface level 0.8 color #5555ff
    3462 
    3463 > volume #3 show style surface level 0.8 color #aa557f
    3464 
    3465 > volume #4 show style surface level 0.8 color #f514fd
    3466 
    3467 > volume #5 show style surface level 0.8 color #11ffcc
    3468 
    3469 > ~display #1
    3470 
    3471 > volume #2 transparency 0.6
    3472 
    3473 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3474 
    3475 > display #1
    3476 
    3477 > volume all region 0,0,0,2129,1523,1744
    3478 
    3479 > ~display #1
    3480 
    3481 > volume #2 show style surface step 2
    3482 
    3483 > volume #3 show style surface step 3
    3484 
    3485 > volume #4 show style surface step 2
    3486 
    3487 > volume #5 show style surface step 2
    3488 
    3489 > volume #5 show style surface step 1
    3490 
    3491 > volume #5 show style surface step 2
    3492 
    3493 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3494 
    3495 > view name p2
    3496 
    3497 > view list
    3498 
    3499 Named views: p1, p2 
    3500 
    3501 > view p1
    3502 
    3503 > view p2
    3504 
    3505 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3506 
    3507 > fly p2 p1 100
    3508 
    3509 > wait
    3510 
    3511 > view p2
    3512 
    3513 > display #1
    3514 
    3515 > volume #1 region 0,0,0,2129,1523,1744
    3516 
    3517 > volume #1 region 0,0,0,2129,1523,1740
    3518 
    3519 > volume #1 region 0,0,0,2129,1523,1742
    3520 
    3521 > volume #1 region 0,0,0,2129,1523,1743
    3522 
    3523 > volume #1 region 0,0,0,2129,1523,1744
    3524 
    3525 > volume #1 region 0,0,0,2129,1523,1743
    3526 
    3527 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3528 
    3529 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    3530 
    3531 opened ChimeraX session 
    3532 
    3533 > display #1
    3534 
    3535 > ~display #2-5
    3536 
    3537 > display #2-5
    3538 
    3539 > ~display #1
    3540 
    3541 > display #1
    3542 
    3543 > ~display #2-5
    3544 
    3545 > volume all region 0,0,0,2129,1523,1743
    3546 
    3547 > display #2-5
    3548 
    3549 > view p2
    3550 
    3551 > lighting soft
    3552 
    3553 > view p1
    3554 
    3555 > help hide
    3556 
    3557 > hide #1
    3558 
    3559 > view p2
    3560 
    3561 > show #2
    3562 
    3563 > volume #2-5 show style surface
    3564 
    3565 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3566 
    3567 > display #1
    3568 
    3569 > ~display #2-5
    3570 
    3571 > volume #2-5 show style surface
    3572 
    3573 > ~display #2-5
    3574 
    3575 > fly p2 p1 100
    3576 
    3577 > wait
    3578 
    3579 > volume #2-5 show style surface transparency 0.5
    3580 
    3581 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    3582 > bgColor black margin 5
    3583 
    3584 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    3585 > bgColor black margin 5
    3586 
    3587 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    3588 > true bgColor black margin 5
    3589 
    3590 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    3591 > true bgColor black margin 5
    3592 
    3593 > volume all planes z,1743,30
    3594 
    3595 > wait 1700
    3596 
    3597 > close session
    3598 
    3599 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    3600 
    3601 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3602 step 1, values int8 
    3603 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3604 shown at level 0.8, step 1, values int8 
    3605 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3606 shown at level 0.8, step 1, values int8 
    3607 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3608 shown at level 0.8, step 1, values int8 
    3609 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3610 shown at level 0.8, step 1, values int8 
    3611 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    3612 © 2016-2022 Regents of the University of California. All rights reserved. 
    3613 How to cite UCSF ChimeraX 
    3614 
    3615 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3616 
    3617 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3618 step 2, values int8 
    3619 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3620 shown at level 0.8, step 2, values int8 
    3621 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3622 shown at level 0.8, step 3, values int8 
    3623 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3624 shown at level 0.8, step 2, values int8 
    3625 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3626 shown at level 0.8, step 2, values int8 
    3627 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    3628 the model panel to edit those fields 
    3629 UCSF ChimeraX version: 1.4 (2022-06-03) 
    3630 © 2016-2022 Regents of the University of California. All rights reserved. 
    3631 How to cite UCSF ChimeraX 
    3632 
    3633 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    3634 
    3635 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3636 step 1, values int8 
    3637 
    3638 > volume showOutlineBox true
    3639 
    3640 > volume region all imageMode "full region"
    3641 
    3642 > volume unzone
    3643 
    3644 > mousemode rightMode "crop volume"
    3645 
    3646 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    3647 > "box faces"
    3648 
    3649 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3650 
    3651 > volume #1 region 0,0,0,1385,1409,1604
    3652 
    3653 > volume #1 region all
    3654 
    3655 > volume #1 region 0,0,0,2129,1523,1748
    3656 
    3657 > view orient
    3658 
    3659 > zoom 0.85
    3660 
    3661 > view name p1
    3662 
    3663 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3664 
    3665 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3666 shown at step 1, values int8 
    3667 
    3668 > close #2
    3669 
    3670 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    3671 
    3672 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3673 shown at step 1, values int8 
    3674 
    3675 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    3676 
    3677 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3678 shown at step 1, values int8 
    3679 
    3680 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3681 
    3682 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3683 shown at step 1, values int8 
    3684 
    3685 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    3686 
    3687 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3688 shown at step 1, values int8 
    3689 
    3690 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3691 
    3692 > volume #2 show style surface level 0.8 color #5555ff
    3693 
    3694 > volume #1 region 0,0,0,2129,1523,1740
    3695 
    3696 > volume all region 0,0,0,2129,1523,1740
    3697 
    3698 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3699 > showOutlineBox true imageMode "box faces"
    3700 
    3701 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3702 > showOutlineBox true imageMode "box faces"
    3703 
    3704 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3705 > showOutlineBox true imageMode "box faces"
    3706 
    3707 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    3708 > faces"
    3709 
    3710 > volume #2 show style surface level -50 color #5555ff
    3711 
    3712 > volume #2 show style surface level 10 color #5555ff
    3713 
    3714 > lighting soft
    3715 
    3716 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3717 
    3718 > volume #2 show style surface level 0.8 color #5555ff
    3719 
    3720 > volume #3 show style surface level 0.8 color #aa557f
    3721 
    3722 > volume #4 show style surface level 0.8 color #f514fd
    3723 
    3724 > volume #5 show style surface level 0.8 color #11ffcc
    3725 
    3726 > ~display #1
    3727 
    3728 > volume #2 transparency 0.6
    3729 
    3730 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3731 
    3732 > display #1
    3733 
    3734 > volume all region 0,0,0,2129,1523,1744
    3735 
    3736 > ~display #1
    3737 
    3738 > volume #2 show style surface step 2
    3739 
    3740 > volume #3 show style surface step 3
    3741 
    3742 > volume #4 show style surface step 2
    3743 
    3744 > volume #5 show style surface step 2
    3745 
    3746 > volume #5 show style surface step 1
    3747 
    3748 > volume #5 show style surface step 2
    3749 
    3750 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3751 
    3752 > view name p2
    3753 
    3754 > view list
    3755 
    3756 Named views: p1, p2 
    3757 
    3758 > view p1
    3759 
    3760 > view p2
    3761 
    3762 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3763 
    3764 > fly p2 p1 100
    3765 
    3766 > wait
    3767 
    3768 > view p2
    3769 
    3770 > display #1
    3771 
    3772 > volume #1 region 0,0,0,2129,1523,1744
    3773 
    3774 > volume #1 region 0,0,0,2129,1523,1740
    3775 
    3776 > volume #1 region 0,0,0,2129,1523,1742
    3777 
    3778 > volume #1 region 0,0,0,2129,1523,1743
    3779 
    3780 > volume #1 region 0,0,0,2129,1523,1744
    3781 
    3782 > volume #1 region 0,0,0,2129,1523,1743
    3783 
    3784 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3785 
    3786 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    3787 
    3788 opened ChimeraX session 
    3789 
    3790 > display #1
    3791 
    3792 > ~display #2-5
    3793 
    3794 > display #2-5
    3795 
    3796 > ~display #1
    3797 
    3798 > display #1
    3799 
    3800 > ~display #2-5
    3801 
    3802 > volume all region 0,0,0,2129,1523,1743
    3803 
    3804 > display #2-5
    3805 
    3806 > view p2
    3807 
    3808 > lighting soft
    3809 
    3810 > view p1
    3811 
    3812 > help hide
    3813 
    3814 > hide #1
    3815 
    3816 > view p2
    3817 
    3818 > show #2
    3819 
    3820 > volume #2-5 show style surface
    3821 
    3822 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3823 
    3824 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    3825 
    3826 opened ChimeraX session 
    3827 
    3828 > display #1
    3829 
    3830 > ~display #2-5
    3831 
    3832 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3833 
    3834 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    3835 
    3836 opened ChimeraX session 
    3837 
    3838 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    3839 
    3840 > fly p2 p1 100
    3841 
    3842 > wait
    3843 
    3844 > volume #2-5 show style surface transparency 0.5
    3845 
    3846 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    3847 > bgColor black margin 5
    3848 
    3849 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    3850 > bgColor black margin 5
    3851 
    3852 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    3853 > true bgColor black margin 5
    3854 
    3855 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    3856 > true bgColor black margin 5
    3857 
    3858 > volume all planes z,1743,30
    3859 
    3860 > wait 1700
    3861 
    3862 > volume #1 hide
    3863 
    3864 > wait 1
    3865 
    3866 > volume #2-5 region all
    3867 
    3868 > wait 1
    3869 
    3870 > volume #3-5 transparency 0
    3871 
    3872 > volume #2 transparency 0.6
    3873 
    3874 > zoom 0.85
    3875 
    3876 > wait 5
    3877 
    3878 > roll y 1 360
    3879 
    3880 > wait
    3881 
    3882 executed F107-A3_session.cxc 
    3883 
    3884 > close session
    3885 
    3886 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    3887 
    3888 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3889 step 1, values int8 
    3890 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3891 shown at step 1, values int8 
    3892 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3893 shown at step 1, values int8 
    3894 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3895 shown at step 1, values int8 
    3896 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3897 shown at step 1, values int8 
    3898 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    3899 © 2016-2022 Regents of the University of California. All rights reserved. 
    3900 How to cite UCSF ChimeraX 
    3901 
    3902 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3903 
    3904 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3905 step 2, values int8 
    3906 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3907 shown at level 0.8, step 2, values int8 
    3908 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3909 shown at level 0.8, step 3, values int8 
    3910 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3911 shown at level 0.8, step 2, values int8 
    3912 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3913 shown at level 0.8, step 2, values int8 
    3914 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    3915 the model panel to edit those fields 
    3916 UCSF ChimeraX version: 1.4 (2022-06-03) 
    3917 © 2016-2022 Regents of the University of California. All rights reserved. 
    3918 How to cite UCSF ChimeraX 
    3919 
    3920 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    3921 
    3922 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    3923 step 1, values int8 
    3924 
    3925 > volume showOutlineBox true
    3926 
    3927 > volume region all imageMode "full region"
    3928 
    3929 > volume unzone
    3930 
    3931 > mousemode rightMode "crop volume"
    3932 
    3933 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    3934 > "box faces"
    3935 
    3936 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3937 
    3938 > volume #1 region 0,0,0,1385,1409,1604
    3939 
    3940 > volume #1 region all
    3941 
    3942 > volume #1 region 0,0,0,2129,1523,1748
    3943 
    3944 > view orient
    3945 
    3946 > zoom 0.85
    3947 
    3948 > view name p1
    3949 
    3950 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3951 
    3952 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3953 shown at step 1, values int8 
    3954 
    3955 > close #2
    3956 
    3957 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    3958 
    3959 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    3960 shown at step 1, values int8 
    3961 
    3962 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    3963 
    3964 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    3965 shown at step 1, values int8 
    3966 
    3967 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    3968 
    3969 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    3970 shown at step 1, values int8 
    3971 
    3972 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    3973 
    3974 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    3975 shown at step 1, values int8 
    3976 
    3977 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    3978 
    3979 > volume #2 show style surface level 0.8 color #5555ff
    3980 
    3981 > volume #1 region 0,0,0,2129,1523,1740
    3982 
    3983 > volume all region 0,0,0,2129,1523,1740
    3984 
    3985 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3986 > showOutlineBox true imageMode "box faces"
    3987 
    3988 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3989 > showOutlineBox true imageMode "box faces"
    3990 
    3991 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    3992 > showOutlineBox true imageMode "box faces"
    3993 
    3994 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    3995 > faces"
    3996 
    3997 > volume #2 show style surface level -50 color #5555ff
    3998 
    3999 > volume #2 show style surface level 10 color #5555ff
    4000 
    4001 > lighting soft
    4002 
    4003 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4004 
    4005 > volume #2 show style surface level 0.8 color #5555ff
    4006 
    4007 > volume #3 show style surface level 0.8 color #aa557f
    4008 
    4009 > volume #4 show style surface level 0.8 color #f514fd
    4010 
    4011 > volume #5 show style surface level 0.8 color #11ffcc
    4012 
    4013 > ~display #1
    4014 
    4015 > volume #2 transparency 0.6
    4016 
    4017 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4018 
    4019 > display #1
    4020 
    4021 > volume all region 0,0,0,2129,1523,1744
    4022 
    4023 > ~display #1
    4024 
    4025 > volume #2 show style surface step 2
    4026 
    4027 > volume #3 show style surface step 3
    4028 
    4029 > volume #4 show style surface step 2
    4030 
    4031 > volume #5 show style surface step 2
    4032 
    4033 > volume #5 show style surface step 1
    4034 
    4035 > volume #5 show style surface step 2
    4036 
    4037 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4038 
    4039 > view name p2
    4040 
    4041 > view list
    4042 
    4043 Named views: p1, p2 
    4044 
    4045 > view p1
    4046 
    4047 > view p2
    4048 
    4049 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4050 
    4051 > fly p2 p1 100
    4052 
    4053 > wait
    4054 
    4055 > view p2
    4056 
    4057 > display #1
    4058 
    4059 > volume #1 region 0,0,0,2129,1523,1744
    4060 
    4061 > volume #1 region 0,0,0,2129,1523,1740
    4062 
    4063 > volume #1 region 0,0,0,2129,1523,1742
    4064 
    4065 > volume #1 region 0,0,0,2129,1523,1743
    4066 
    4067 > volume #1 region 0,0,0,2129,1523,1744
    4068 
    4069 > volume #1 region 0,0,0,2129,1523,1743
    4070 
    4071 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4072 
    4073 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    4074 
    4075 opened ChimeraX session 
    4076 
    4077 > display #1
    4078 
    4079 > ~display #2-5
    4080 
    4081 > display #2-5
    4082 
    4083 > ~display #1
    4084 
    4085 > display #1
    4086 
    4087 > ~display #2-5
    4088 
    4089 > volume all region 0,0,0,2129,1523,1743
    4090 
    4091 > display #2-5
    4092 
    4093 > view p2
    4094 
    4095 > lighting soft
    4096 
    4097 > view p1
    4098 
    4099 > help hide
    4100 
    4101 > hide #1
    4102 
    4103 > view p2
    4104 
    4105 > show #2
    4106 
    4107 > volume #2-5 show style surface
    4108 
    4109 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4110 
    4111 > display #1
    4112 
    4113 > ~display #2-5
    4114 
    4115 > volume #2-5 show style surface
    4116 
    4117 > ~display #2-5
    4118 
    4119 > fly p2 p1 100
    4120 
    4121 > wait
    4122 
    4123 > volume #2-5 show style surface transparency 0.5
    4124 
    4125 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    4126 > bgColor black margin 5
    4127 
    4128 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    4129 > bgColor black margin 5
    4130 
    4131 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    4132 > true bgColor black margin 5
    4133 
    4134 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    4135 > true bgColor black margin 5
    4136 
    4137 > volume all planes z,1743,30
    4138 
    4139 > wait 1700
    4140 
    4141 > close session
    4142 
    4143 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    4144 
    4145 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4146 step 1, values int8 
    4147 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4148 shown at level 0.8, step 1, values int8 
    4149 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4150 shown at level 0.8, step 1, values int8 
    4151 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4152 shown at level 0.8, step 1, values int8 
    4153 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4154 shown at level 0.8, step 1, values int8 
    4155 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    4156 © 2016-2022 Regents of the University of California. All rights reserved. 
    4157 How to cite UCSF ChimeraX 
    4158 
    4159 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4160 
    4161 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4162 step 2, values int8 
    4163 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4164 shown at level 0.8, step 2, values int8 
    4165 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4166 shown at level 0.8, step 3, values int8 
    4167 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4168 shown at level 0.8, step 2, values int8 
    4169 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4170 shown at level 0.8, step 2, values int8 
    4171 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    4172 the model panel to edit those fields 
    4173 UCSF ChimeraX version: 1.4 (2022-06-03) 
    4174 © 2016-2022 Regents of the University of California. All rights reserved. 
    4175 How to cite UCSF ChimeraX 
    4176 
    4177 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    4178 
    4179 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4180 step 1, values int8 
    4181 
    4182 > volume showOutlineBox true
    4183 
    4184 > volume region all imageMode "full region"
    4185 
    4186 > volume unzone
    4187 
    4188 > mousemode rightMode "crop volume"
    4189 
    4190 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    4191 > "box faces"
    4192 
    4193 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4194 
    4195 > volume #1 region 0,0,0,1385,1409,1604
    4196 
    4197 > volume #1 region all
    4198 
    4199 > volume #1 region 0,0,0,2129,1523,1748
    4200 
    4201 > view orient
    4202 
    4203 > zoom 0.85
    4204 
    4205 > view name p1
    4206 
    4207 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4208 
    4209 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4210 shown at step 1, values int8 
    4211 
    4212 > close #2
    4213 
    4214 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    4215 
    4216 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4217 shown at step 1, values int8 
    4218 
    4219 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    4220 
    4221 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4222 shown at step 1, values int8 
    4223 
    4224 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4225 
    4226 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4227 shown at step 1, values int8 
    4228 
    4229 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    4230 
    4231 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4232 shown at step 1, values int8 
    4233 
    4234 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4235 
    4236 > volume #2 show style surface level 0.8 color #5555ff
    4237 
    4238 > volume #1 region 0,0,0,2129,1523,1740
    4239 
    4240 > volume all region 0,0,0,2129,1523,1740
    4241 
    4242 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4243 > showOutlineBox true imageMode "box faces"
    4244 
    4245 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4246 > showOutlineBox true imageMode "box faces"
    4247 
    4248 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4249 > showOutlineBox true imageMode "box faces"
    4250 
    4251 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    4252 > faces"
    4253 
    4254 > volume #2 show style surface level -50 color #5555ff
    4255 
    4256 > volume #2 show style surface level 10 color #5555ff
    4257 
    4258 > lighting soft
    4259 
    4260 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4261 
    4262 > volume #2 show style surface level 0.8 color #5555ff
    4263 
    4264 > volume #3 show style surface level 0.8 color #aa557f
    4265 
    4266 > volume #4 show style surface level 0.8 color #f514fd
    4267 
    4268 > volume #5 show style surface level 0.8 color #11ffcc
    4269 
    4270 > ~display #1
    4271 
    4272 > volume #2 transparency 0.6
    4273 
    4274 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4275 
    4276 > display #1
    4277 
    4278 > volume all region 0,0,0,2129,1523,1744
    4279 
    4280 > ~display #1
    4281 
    4282 > volume #2 show style surface step 2
    4283 
    4284 > volume #3 show style surface step 3
    4285 
    4286 > volume #4 show style surface step 2
    4287 
    4288 > volume #5 show style surface step 2
    4289 
    4290 > volume #5 show style surface step 1
    4291 
    4292 > volume #5 show style surface step 2
    4293 
    4294 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4295 
    4296 > view name p2
    4297 
    4298 > view list
    4299 
    4300 Named views: p1, p2 
    4301 
    4302 > view p1
    4303 
    4304 > view p2
    4305 
    4306 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4307 
    4308 > fly p2 p1 100
    4309 
    4310 > wait
    4311 
    4312 > view p2
    4313 
    4314 > display #1
    4315 
    4316 > volume #1 region 0,0,0,2129,1523,1744
    4317 
    4318 > volume #1 region 0,0,0,2129,1523,1740
    4319 
    4320 > volume #1 region 0,0,0,2129,1523,1742
    4321 
    4322 > volume #1 region 0,0,0,2129,1523,1743
    4323 
    4324 > volume #1 region 0,0,0,2129,1523,1744
    4325 
    4326 > volume #1 region 0,0,0,2129,1523,1743
    4327 
    4328 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4329 
    4330 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    4331 
    4332 opened ChimeraX session 
    4333 
    4334 > display #1
    4335 
    4336 > ~display #2-5
    4337 
    4338 > display #2-5
    4339 
    4340 > ~display #1
    4341 
    4342 > display #1
    4343 
    4344 > ~display #2-5
    4345 
    4346 > volume all region 0,0,0,2129,1523,1743
    4347 
    4348 > display #2-5
    4349 
    4350 > view p2
    4351 
    4352 > lighting soft
    4353 
    4354 > view p1
    4355 
    4356 > help hide
    4357 
    4358 > hide #1
    4359 
    4360 > view p2
    4361 
    4362 > show #2
    4363 
    4364 > volume #2-5 show style surface
    4365 
    4366 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4367 
    4368 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    4369 
    4370 opened ChimeraX session 
    4371 
    4372 > display #1
    4373 
    4374 > ~display #2-5
    4375 
    4376 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4377 
    4378 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    4379 
    4380 opened ChimeraX session 
    4381 
    4382 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    4383 
    4384 > fly p2 p1 100
    4385 
    4386 > wait
    4387 
    4388 > volume #2-5 show style surface transparency 0.5
    4389 
    4390 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    4391 > bgColor black margin 5
    4392 
    4393 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    4394 > bgColor black margin 5
    4395 
    4396 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    4397 > true bgColor black margin 5
    4398 
    4399 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    4400 > true bgColor black margin 5
    4401 
    4402 > volume all planes z,1743,30
    4403 
    4404 > wait 1743
    4405 
    4406 > volume #1 hide
    4407 
    4408 > wait 1
    4409 
    4410 > volume #2-5 region all
    4411 
    4412 > wait 1
    4413 
    4414 > volume #3-5 transparency 0
    4415 
    4416 > volume #2 transparency 0.6
    4417 
    4418 executed F107-A3_session.cxc 
    4419 
    4420 > zoom 0.85
    4421 
    4422 > wait 5
    4423 
    4424 > oll y 1 360; wait;
    4425 
    4426 Unknown command: oll y 1 360; wait; 
    4427 
    4428 > roll y 1 360
    4429 
    4430 > wait
    4431 
    4432 > fly p1 p2 100
    4433 
    4434 > wait
    4435 
    4436 > view p1
    4437 
    4438 > roll y 1 360
    4439 
    4440 > wait
    4441 
    4442 > fly p1 p2 100
    4443 
    4444 > wait
    4445 
    4446 > close session
    4447 
    4448 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    4449 
    4450 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4451 step 1, values int8 
    4452 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4453 shown at step 1, values int8 
    4454 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4455 shown at step 1, values int8 
    4456 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4457 shown at step 1, values int8 
    4458 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4459 shown at step 1, values int8 
    4460 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    4461 © 2016-2022 Regents of the University of California. All rights reserved. 
    4462 How to cite UCSF ChimeraX 
    4463 
    4464 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4465 
    4466 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4467 step 2, values int8 
    4468 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4469 shown at level 0.8, step 2, values int8 
    4470 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4471 shown at level 0.8, step 3, values int8 
    4472 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4473 shown at level 0.8, step 2, values int8 
    4474 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4475 shown at level 0.8, step 2, values int8 
    4476 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    4477 the model panel to edit those fields 
    4478 UCSF ChimeraX version: 1.4 (2022-06-03) 
    4479 © 2016-2022 Regents of the University of California. All rights reserved. 
    4480 How to cite UCSF ChimeraX 
    4481 
    4482 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    4483 
    4484 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4485 step 1, values int8 
    4486 
    4487 > volume showOutlineBox true
    4488 
    4489 > volume region all imageMode "full region"
    4490 
    4491 > volume unzone
    4492 
    4493 > mousemode rightMode "crop volume"
    4494 
    4495 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    4496 > "box faces"
    4497 
    4498 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4499 
    4500 > volume #1 region 0,0,0,1385,1409,1604
    4501 
    4502 > volume #1 region all
    4503 
    4504 > volume #1 region 0,0,0,2129,1523,1748
    4505 
    4506 > view orient
    4507 
    4508 > zoom 0.85
    4509 
    4510 > view name p1
    4511 
    4512 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4513 
    4514 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4515 shown at step 1, values int8 
    4516 
    4517 > close #2
    4518 
    4519 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    4520 
    4521 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4522 shown at step 1, values int8 
    4523 
    4524 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    4525 
    4526 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4527 shown at step 1, values int8 
    4528 
    4529 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4530 
    4531 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4532 shown at step 1, values int8 
    4533 
    4534 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    4535 
    4536 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4537 shown at step 1, values int8 
    4538 
    4539 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4540 
    4541 > volume #2 show style surface level 0.8 color #5555ff
    4542 
    4543 > volume #1 region 0,0,0,2129,1523,1740
    4544 
    4545 > volume all region 0,0,0,2129,1523,1740
    4546 
    4547 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4548 > showOutlineBox true imageMode "box faces"
    4549 
    4550 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4551 > showOutlineBox true imageMode "box faces"
    4552 
    4553 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4554 > showOutlineBox true imageMode "box faces"
    4555 
    4556 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    4557 > faces"
    4558 
    4559 > volume #2 show style surface level -50 color #5555ff
    4560 
    4561 > volume #2 show style surface level 10 color #5555ff
    4562 
    4563 > lighting soft
    4564 
    4565 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4566 
    4567 > volume #2 show style surface level 0.8 color #5555ff
    4568 
    4569 > volume #3 show style surface level 0.8 color #aa557f
    4570 
    4571 > volume #4 show style surface level 0.8 color #f514fd
    4572 
    4573 > volume #5 show style surface level 0.8 color #11ffcc
    4574 
    4575 > ~display #1
    4576 
    4577 > volume #2 transparency 0.6
    4578 
    4579 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4580 
    4581 > display #1
    4582 
    4583 > volume all region 0,0,0,2129,1523,1744
    4584 
    4585 > ~display #1
    4586 
    4587 > volume #2 show style surface step 2
    4588 
    4589 > volume #3 show style surface step 3
    4590 
    4591 > volume #4 show style surface step 2
    4592 
    4593 > volume #5 show style surface step 2
    4594 
    4595 > volume #5 show style surface step 1
    4596 
    4597 > volume #5 show style surface step 2
    4598 
    4599 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4600 
    4601 > view name p2
    4602 
    4603 > view list
    4604 
    4605 Named views: p1, p2 
    4606 
    4607 > view p1
    4608 
    4609 > view p2
    4610 
    4611 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4612 
    4613 > fly p2 p1 100
    4614 
    4615 > wait
    4616 
    4617 > view p2
    4618 
    4619 > display #1
    4620 
    4621 > volume #1 region 0,0,0,2129,1523,1744
    4622 
    4623 > volume #1 region 0,0,0,2129,1523,1740
    4624 
    4625 > volume #1 region 0,0,0,2129,1523,1742
    4626 
    4627 > volume #1 region 0,0,0,2129,1523,1743
    4628 
    4629 > volume #1 region 0,0,0,2129,1523,1744
    4630 
    4631 > volume #1 region 0,0,0,2129,1523,1743
    4632 
    4633 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4634 
    4635 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    4636 
    4637 opened ChimeraX session 
    4638 
    4639 > display #1
    4640 
    4641 > ~display #2-5
    4642 
    4643 > display #2-5
    4644 
    4645 > ~display #1
    4646 
    4647 > display #1
    4648 
    4649 > ~display #2-5
    4650 
    4651 > volume all region 0,0,0,2129,1523,1743
    4652 
    4653 > display #2-5
    4654 
    4655 > view p2
    4656 
    4657 > lighting soft
    4658 
    4659 > view p1
    4660 
    4661 > help hide
    4662 
    4663 > hide #1
    4664 
    4665 > view p2
    4666 
    4667 > show #2
    4668 
    4669 > volume #2-5 show style surface
    4670 
    4671 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4672 
    4673 > display #1
    4674 
    4675 > ~display #2-5
    4676 
    4677 > volume #2-5 show style surface
    4678 
    4679 > ~display #2-5
    4680 
    4681 > fly p2 p1 100
    4682 
    4683 > wait
    4684 
    4685 > volume #2-5 show style surface transparency 0.5
    4686 
    4687 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    4688 > bgColor black margin 5
    4689 
    4690 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    4691 > bgColor black margin 5
    4692 
    4693 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    4694 > true bgColor black margin 5
    4695 
    4696 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    4697 > true bgColor black margin 5
    4698 
    4699 > volume all planes z,1743,30
    4700 
    4701 > wait 1700
    4702 
    4703 > close session
    4704 
    4705 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    4706 
    4707 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4708 step 1, values int8 
    4709 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4710 shown at level 0.8, step 1, values int8 
    4711 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4712 shown at level 0.8, step 1, values int8 
    4713 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4714 shown at level 0.8, step 1, values int8 
    4715 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4716 shown at level 0.8, step 1, values int8 
    4717 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    4718 © 2016-2022 Regents of the University of California. All rights reserved. 
    4719 How to cite UCSF ChimeraX 
    4720 
    4721 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4722 
    4723 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4724 step 2, values int8 
    4725 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4726 shown at level 0.8, step 2, values int8 
    4727 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4728 shown at level 0.8, step 3, values int8 
    4729 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4730 shown at level 0.8, step 2, values int8 
    4731 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4732 shown at level 0.8, step 2, values int8 
    4733 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    4734 the model panel to edit those fields 
    4735 UCSF ChimeraX version: 1.4 (2022-06-03) 
    4736 © 2016-2022 Regents of the University of California. All rights reserved. 
    4737 How to cite UCSF ChimeraX 
    4738 
    4739 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    4740 
    4741 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4742 step 1, values int8 
    4743 
    4744 > volume showOutlineBox true
    4745 
    4746 > volume region all imageMode "full region"
    4747 
    4748 > volume unzone
    4749 
    4750 > mousemode rightMode "crop volume"
    4751 
    4752 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    4753 > "box faces"
    4754 
    4755 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4756 
    4757 > volume #1 region 0,0,0,1385,1409,1604
    4758 
    4759 > volume #1 region all
    4760 
    4761 > volume #1 region 0,0,0,2129,1523,1748
    4762 
    4763 > view orient
    4764 
    4765 > zoom 0.85
    4766 
    4767 > view name p1
    4768 
    4769 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4770 
    4771 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4772 shown at step 1, values int8 
    4773 
    4774 > close #2
    4775 
    4776 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    4777 
    4778 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4779 shown at step 1, values int8 
    4780 
    4781 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    4782 
    4783 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4784 shown at step 1, values int8 
    4785 
    4786 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    4787 
    4788 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    4789 shown at step 1, values int8 
    4790 
    4791 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    4792 
    4793 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    4794 shown at step 1, values int8 
    4795 
    4796 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4797 
    4798 > volume #2 show style surface level 0.8 color #5555ff
    4799 
    4800 > volume #1 region 0,0,0,2129,1523,1740
    4801 
    4802 > volume all region 0,0,0,2129,1523,1740
    4803 
    4804 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4805 > showOutlineBox true imageMode "box faces"
    4806 
    4807 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4808 > showOutlineBox true imageMode "box faces"
    4809 
    4810 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    4811 > showOutlineBox true imageMode "box faces"
    4812 
    4813 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    4814 > faces"
    4815 
    4816 > volume #2 show style surface level -50 color #5555ff
    4817 
    4818 > volume #2 show style surface level 10 color #5555ff
    4819 
    4820 > lighting soft
    4821 
    4822 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4823 
    4824 > volume #2 show style surface level 0.8 color #5555ff
    4825 
    4826 > volume #3 show style surface level 0.8 color #aa557f
    4827 
    4828 > volume #4 show style surface level 0.8 color #f514fd
    4829 
    4830 > volume #5 show style surface level 0.8 color #11ffcc
    4831 
    4832 > ~display #1
    4833 
    4834 > volume #2 transparency 0.6
    4835 
    4836 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4837 
    4838 > display #1
    4839 
    4840 > volume all region 0,0,0,2129,1523,1744
    4841 
    4842 > ~display #1
    4843 
    4844 > volume #2 show style surface step 2
    4845 
    4846 > volume #3 show style surface step 3
    4847 
    4848 > volume #4 show style surface step 2
    4849 
    4850 > volume #5 show style surface step 2
    4851 
    4852 > volume #5 show style surface step 1
    4853 
    4854 > volume #5 show style surface step 2
    4855 
    4856 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4857 
    4858 > view name p2
    4859 
    4860 > view list
    4861 
    4862 Named views: p1, p2 
    4863 
    4864 > view p1
    4865 
    4866 > view p2
    4867 
    4868 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4869 
    4870 > fly p2 p1 100
    4871 
    4872 > wait
    4873 
    4874 > view p2
    4875 
    4876 > display #1
    4877 
    4878 > volume #1 region 0,0,0,2129,1523,1744
    4879 
    4880 > volume #1 region 0,0,0,2129,1523,1740
    4881 
    4882 > volume #1 region 0,0,0,2129,1523,1742
    4883 
    4884 > volume #1 region 0,0,0,2129,1523,1743
    4885 
    4886 > volume #1 region 0,0,0,2129,1523,1744
    4887 
    4888 > volume #1 region 0,0,0,2129,1523,1743
    4889 
    4890 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4891 
    4892 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    4893 
    4894 opened ChimeraX session 
    4895 
    4896 > display #1
    4897 
    4898 > ~display #2-5
    4899 
    4900 > display #2-5
    4901 
    4902 > ~display #1
    4903 
    4904 > display #1
    4905 
    4906 > ~display #2-5
    4907 
    4908 > volume all region 0,0,0,2129,1523,1743
    4909 
    4910 > display #2-5
    4911 
    4912 > view p2
    4913 
    4914 > lighting soft
    4915 
    4916 > view p1
    4917 
    4918 > help hide
    4919 
    4920 > hide #1
    4921 
    4922 > view p2
    4923 
    4924 > show #2
    4925 
    4926 > volume #2-5 show style surface
    4927 
    4928 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4929 
    4930 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    4931 
    4932 opened ChimeraX session 
    4933 
    4934 > display #1
    4935 
    4936 > ~display #2-5
    4937 
    4938 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    4939 
    4940 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    4941 
    4942 opened ChimeraX session 
    4943 
    4944 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    4945 
    4946 > fly p2 p1 100
    4947 
    4948 > wait
    4949 
    4950 > volume #2-5 show style surface transparency 0.5
    4951 
    4952 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    4953 > bgColor black margin 5
    4954 
    4955 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    4956 > bgColor black margin 5
    4957 
    4958 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    4959 > true bgColor black margin 5
    4960 
    4961 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    4962 > true bgColor black margin 5
    4963 
    4964 > volume all planes z,1743,30
    4965 
    4966 > wait 1743
    4967 
    4968 > volume #1 hide
    4969 
    4970 > wait 1
    4971 
    4972 > volume #2-5 region all
    4973 
    4974 > wait 1
    4975 
    4976 > volume #3-5 transparency 0
    4977 
    4978 > volume #2 transparency 0.6
    4979 
    4980 > roll y 1 360
    4981 
    4982 > wait
    4983 
    4984 > fly p1 p2 100
    4985 
    4986 > wait
    4987 
    4988 executed F107-A3_session.cxc 
    4989 
    4990 > close session
    4991 
    4992 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    4993 
    4994 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    4995 step 1, values int8 
    4996 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    4997 shown at step 1, values int8 
    4998 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    4999 shown at step 1, values int8 
    5000 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5001 shown at step 1, values int8 
    5002 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5003 shown at step 1, values int8 
    5004 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    5005 © 2016-2022 Regents of the University of California. All rights reserved. 
    5006 How to cite UCSF ChimeraX 
    5007 
    5008 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5009 
    5010 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5011 step 2, values int8 
    5012 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5013 shown at level 0.8, step 2, values int8 
    5014 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5015 shown at level 0.8, step 3, values int8 
    5016 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5017 shown at level 0.8, step 2, values int8 
    5018 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5019 shown at level 0.8, step 2, values int8 
    5020 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    5021 the model panel to edit those fields 
    5022 UCSF ChimeraX version: 1.4 (2022-06-03) 
    5023 © 2016-2022 Regents of the University of California. All rights reserved. 
    5024 How to cite UCSF ChimeraX 
    5025 
    5026 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    5027 
    5028 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5029 step 1, values int8 
    5030 
    5031 > volume showOutlineBox true
    5032 
    5033 > volume region all imageMode "full region"
    5034 
    5035 > volume unzone
    5036 
    5037 > mousemode rightMode "crop volume"
    5038 
    5039 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    5040 > "box faces"
    5041 
    5042 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5043 
    5044 > volume #1 region 0,0,0,1385,1409,1604
    5045 
    5046 > volume #1 region all
    5047 
    5048 > volume #1 region 0,0,0,2129,1523,1748
    5049 
    5050 > view orient
    5051 
    5052 > zoom 0.85
    5053 
    5054 > view name p1
    5055 
    5056 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5057 
    5058 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5059 shown at step 1, values int8 
    5060 
    5061 > close #2
    5062 
    5063 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    5064 
    5065 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5066 shown at step 1, values int8 
    5067 
    5068 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    5069 
    5070 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5071 shown at step 1, values int8 
    5072 
    5073 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5074 
    5075 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5076 shown at step 1, values int8 
    5077 
    5078 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    5079 
    5080 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5081 shown at step 1, values int8 
    5082 
    5083 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5084 
    5085 > volume #2 show style surface level 0.8 color #5555ff
    5086 
    5087 > volume #1 region 0,0,0,2129,1523,1740
    5088 
    5089 > volume all region 0,0,0,2129,1523,1740
    5090 
    5091 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5092 > showOutlineBox true imageMode "box faces"
    5093 
    5094 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5095 > showOutlineBox true imageMode "box faces"
    5096 
    5097 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5098 > showOutlineBox true imageMode "box faces"
    5099 
    5100 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    5101 > faces"
    5102 
    5103 > volume #2 show style surface level -50 color #5555ff
    5104 
    5105 > volume #2 show style surface level 10 color #5555ff
    5106 
    5107 > lighting soft
    5108 
    5109 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5110 
    5111 > volume #2 show style surface level 0.8 color #5555ff
    5112 
    5113 > volume #3 show style surface level 0.8 color #aa557f
    5114 
    5115 > volume #4 show style surface level 0.8 color #f514fd
    5116 
    5117 > volume #5 show style surface level 0.8 color #11ffcc
    5118 
    5119 > ~display #1
    5120 
    5121 > volume #2 transparency 0.6
    5122 
    5123 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5124 
    5125 > display #1
    5126 
    5127 > volume all region 0,0,0,2129,1523,1744
    5128 
    5129 > ~display #1
    5130 
    5131 > volume #2 show style surface step 2
    5132 
    5133 > volume #3 show style surface step 3
    5134 
    5135 > volume #4 show style surface step 2
    5136 
    5137 > volume #5 show style surface step 2
    5138 
    5139 > volume #5 show style surface step 1
    5140 
    5141 > volume #5 show style surface step 2
    5142 
    5143 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5144 
    5145 > view name p2
    5146 
    5147 > view list
    5148 
    5149 Named views: p1, p2 
    5150 
    5151 > view p1
    5152 
    5153 > view p2
    5154 
    5155 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5156 
    5157 > fly p2 p1 100
    5158 
    5159 > wait
    5160 
    5161 > view p2
    5162 
    5163 > display #1
    5164 
    5165 > volume #1 region 0,0,0,2129,1523,1744
    5166 
    5167 > volume #1 region 0,0,0,2129,1523,1740
    5168 
    5169 > volume #1 region 0,0,0,2129,1523,1742
    5170 
    5171 > volume #1 region 0,0,0,2129,1523,1743
    5172 
    5173 > volume #1 region 0,0,0,2129,1523,1744
    5174 
    5175 > volume #1 region 0,0,0,2129,1523,1743
    5176 
    5177 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5178 
    5179 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    5180 
    5181 opened ChimeraX session 
    5182 
    5183 > display #1
    5184 
    5185 > ~display #2-5
    5186 
    5187 > display #2-5
    5188 
    5189 > ~display #1
    5190 
    5191 > display #1
    5192 
    5193 > ~display #2-5
    5194 
    5195 > volume all region 0,0,0,2129,1523,1743
    5196 
    5197 > display #2-5
    5198 
    5199 > view p2
    5200 
    5201 > lighting soft
    5202 
    5203 > view p1
    5204 
    5205 > help hide
    5206 
    5207 > hide #1
    5208 
    5209 > view p2
    5210 
    5211 > show #2
    5212 
    5213 > volume #2-5 show style surface
    5214 
    5215 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5216 
    5217 > display #1
    5218 
    5219 > ~display #2-5
    5220 
    5221 > volume #2-5 show style surface
    5222 
    5223 > ~display #2-5
    5224 
    5225 > fly p2 p1 100
    5226 
    5227 > wait
    5228 
    5229 > volume #2-5 show style surface transparency 0.5
    5230 
    5231 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    5232 > bgColor black margin 5
    5233 
    5234 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    5235 > bgColor black margin 5
    5236 
    5237 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    5238 > true bgColor black margin 5
    5239 
    5240 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    5241 > true bgColor black margin 5
    5242 
    5243 > volume all planes z,1743,30
    5244 
    5245 > wait 1700
    5246 
    5247 > close session
    5248 
    5249 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    5250 
    5251 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5252 step 1, values int8 
    5253 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5254 shown at level 0.8, step 1, values int8 
    5255 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5256 shown at level 0.8, step 1, values int8 
    5257 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5258 shown at level 0.8, step 1, values int8 
    5259 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5260 shown at level 0.8, step 1, values int8 
    5261 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    5262 © 2016-2022 Regents of the University of California. All rights reserved. 
    5263 How to cite UCSF ChimeraX 
    5264 
    5265 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5266 
    5267 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5268 step 2, values int8 
    5269 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5270 shown at level 0.8, step 2, values int8 
    5271 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5272 shown at level 0.8, step 3, values int8 
    5273 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5274 shown at level 0.8, step 2, values int8 
    5275 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5276 shown at level 0.8, step 2, values int8 
    5277 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    5278 the model panel to edit those fields 
    5279 UCSF ChimeraX version: 1.4 (2022-06-03) 
    5280 © 2016-2022 Regents of the University of California. All rights reserved. 
    5281 How to cite UCSF ChimeraX 
    5282 
    5283 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    5284 
    5285 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5286 step 1, values int8 
    5287 
    5288 > volume showOutlineBox true
    5289 
    5290 > volume region all imageMode "full region"
    5291 
    5292 > volume unzone
    5293 
    5294 > mousemode rightMode "crop volume"
    5295 
    5296 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    5297 > "box faces"
    5298 
    5299 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5300 
    5301 > volume #1 region 0,0,0,1385,1409,1604
    5302 
    5303 > volume #1 region all
    5304 
    5305 > volume #1 region 0,0,0,2129,1523,1748
    5306 
    5307 > view orient
    5308 
    5309 > zoom 0.85
    5310 
    5311 > view name p1
    5312 
    5313 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5314 
    5315 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5316 shown at step 1, values int8 
    5317 
    5318 > close #2
    5319 
    5320 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    5321 
    5322 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5323 shown at step 1, values int8 
    5324 
    5325 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    5326 
    5327 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5328 shown at step 1, values int8 
    5329 
    5330 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5331 
    5332 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5333 shown at step 1, values int8 
    5334 
    5335 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    5336 
    5337 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5338 shown at step 1, values int8 
    5339 
    5340 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5341 
    5342 > volume #2 show style surface level 0.8 color #5555ff
    5343 
    5344 > volume #1 region 0,0,0,2129,1523,1740
    5345 
    5346 > volume all region 0,0,0,2129,1523,1740
    5347 
    5348 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5349 > showOutlineBox true imageMode "box faces"
    5350 
    5351 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5352 > showOutlineBox true imageMode "box faces"
    5353 
    5354 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5355 > showOutlineBox true imageMode "box faces"
    5356 
    5357 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    5358 > faces"
    5359 
    5360 > volume #2 show style surface level -50 color #5555ff
    5361 
    5362 > volume #2 show style surface level 10 color #5555ff
    5363 
    5364 > lighting soft
    5365 
    5366 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5367 
    5368 > volume #2 show style surface level 0.8 color #5555ff
    5369 
    5370 > volume #3 show style surface level 0.8 color #aa557f
    5371 
    5372 > volume #4 show style surface level 0.8 color #f514fd
    5373 
    5374 > volume #5 show style surface level 0.8 color #11ffcc
    5375 
    5376 > ~display #1
    5377 
    5378 > volume #2 transparency 0.6
    5379 
    5380 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5381 
    5382 > display #1
    5383 
    5384 > volume all region 0,0,0,2129,1523,1744
    5385 
    5386 > ~display #1
    5387 
    5388 > volume #2 show style surface step 2
    5389 
    5390 > volume #3 show style surface step 3
    5391 
    5392 > volume #4 show style surface step 2
    5393 
    5394 > volume #5 show style surface step 2
    5395 
    5396 > volume #5 show style surface step 1
    5397 
    5398 > volume #5 show style surface step 2
    5399 
    5400 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5401 
    5402 > view name p2
    5403 
    5404 > view list
    5405 
    5406 Named views: p1, p2 
    5407 
    5408 > view p1
    5409 
    5410 > view p2
    5411 
    5412 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5413 
    5414 > fly p2 p1 100
    5415 
    5416 > wait
    5417 
    5418 > view p2
    5419 
    5420 > display #1
    5421 
    5422 > volume #1 region 0,0,0,2129,1523,1744
    5423 
    5424 > volume #1 region 0,0,0,2129,1523,1740
    5425 
    5426 > volume #1 region 0,0,0,2129,1523,1742
    5427 
    5428 > volume #1 region 0,0,0,2129,1523,1743
    5429 
    5430 > volume #1 region 0,0,0,2129,1523,1744
    5431 
    5432 > volume #1 region 0,0,0,2129,1523,1743
    5433 
    5434 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5435 
    5436 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    5437 
    5438 opened ChimeraX session 
    5439 
    5440 > display #1
    5441 
    5442 > ~display #2-5
    5443 
    5444 > display #2-5
    5445 
    5446 > ~display #1
    5447 
    5448 > display #1
    5449 
    5450 > ~display #2-5
    5451 
    5452 > volume all region 0,0,0,2129,1523,1743
    5453 
    5454 > display #2-5
    5455 
    5456 > view p2
    5457 
    5458 > lighting soft
    5459 
    5460 > view p1
    5461 
    5462 > help hide
    5463 
    5464 > hide #1
    5465 
    5466 > view p2
    5467 
    5468 > show #2
    5469 
    5470 > volume #2-5 show style surface
    5471 
    5472 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5473 
    5474 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    5475 
    5476 opened ChimeraX session 
    5477 
    5478 > display #1
    5479 
    5480 > ~display #2-5
    5481 
    5482 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5483 
    5484 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    5485 
    5486 opened ChimeraX session 
    5487 
    5488 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    5489 
    5490 > movie record supersample 3
    5491 
    5492 > fly p2 p1 100
    5493 
    5494 > wait
    5495 
    5496 > volume #2-5 show style surface transparency 0.5
    5497 
    5498 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    5499 > bgColor black margin 5
    5500 
    5501 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    5502 > bgColor black margin 5
    5503 
    5504 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    5505 > true bgColor black margin 5
    5506 
    5507 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    5508 > true bgColor black margin 5
    5509 
    5510 > volume all planes z,1743,30
    5511 
    5512 > wait 1743
    5513 
    5514 > volume #1 hide
    5515 
    5516 > wait 1
    5517 
    5518 > volume #2-5 region all
    5519 
    5520 > wait 1
    5521 
    5522 > volume #3-5 transparency 0
    5523 
    5524 > volume #2 transparency 0.6
    5525 
    5526 > roll y 1 360
    5527 
    5528 > wait
    5529 
    5530 > fly p1 p2 100
    5531 
    5532 > wait
    5533 
    5534 > perframe "volume all region 0,0,0,2129,1523,$1" ranges 1743,30
    5535 
    5536 > wait 1720
    5537 
    5538 > movie encode framerate 25 quality good output
    5539 > /tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4 verbose true
    5540 > format h264 wait true
    5541 
    5542 /usr/libexec/UCSF-ChimeraX/bin/ffmpeg -r 25.0 -i /tmp/chimovie_mNsA-%05d.ppm
    5543 -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4
    5544 -pix_fmt yuv420p -crf 20
    5545 /tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4 
    5546 stdout: 
    5547  
    5548 stderr: 
    5549 ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers 
    5550 built with gcc 8 (GCC) 
    5551 configuration: --prefix=/tmp/chx-v1.4.jOWCxR/build --enable-gpl --enable-
    5552 version3 --disable-network --disable-doc --disable-devices --disable-ffplay
    5553 --disable-ffserver --disable-ffprobe --enable-libtheora --enable-libvpx
    5554 --enable-libx264 --yasmexe=/tmp/chx-v1.4.jOWCxR/build/bin/yasm --optflags=-O
    5555 --extra-cflags=-I/tmp/chx-v1.4.jOWCxR/build/include --extra-ldflags='-O3 -Wall
    5556 -Wextra -D_FORTIFY=2 -L/tmp/chx-v1.4.jOWCxR/build/lib' --extra-libs=-ldl 
    5557 libavutil 55. 34.101 / 55. 34.101 
    5558 libavcodec 57. 64.101 / 57. 64.101 
    5559 libavformat 57. 56.101 / 57. 56.101 
    5560 libavdevice 57. 1.100 / 57. 1.100 
    5561 libavfilter 6. 65.100 / 6. 65.100 
    5562 libswscale 4. 2.100 / 4. 2.100 
    5563 libswresample 2. 3.100 / 2. 3.100 
    5564 libpostproc 54. 1.100 / 54. 1.100 
    5565 Input #0, image2, from '/tmp/chimovie_mNsA-%05d.ppm': 
    5566 Duration: 00:02:41.16, start: 0.000000, bitrate: N/A 
    5567 Stream #0:0: Video: ppm, rgb24, 1708x1033, 25 tbr, 25 tbn, 25 tbc 
    5568 [libx264 @ 0x2f41260] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
    5569 FMA3 AVX2 LZCNT BMI2 
    5570 [libx264 @ 0x2f41260] profile High, level 4.0 
    5571 [libx264 @ 0x2f41260] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
    5572 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
    5573 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
    5574 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
    5575 fast_pskip=1 chroma_qp_offset=-2 threads=32 lookahead_threads=5
    5576 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
    5577 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
    5578 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
    5579 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
    5580 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 
    5581 Output #0, mp4, to
    5582 '/tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4': 
    5583 Metadata: 
    5584 encoder : Lavf57.56.101 
    5585 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
    5586 1708x1032, q=-1--1, 25 fps, 12800 tbn, 25 tbc 
    5587 Metadata: 
    5588 encoder : Lavc57.64.101 libx264 
    5589 Side data: 
    5590 cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 
    5591 Stream mapping: 
    5592 Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) 
    5593 Press [q] to stop, [?] for help 
    5594 frame= 74 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
    5595 frame= 156 fps=155 q=25.0 size= 1664kB time=00:00:03.08 bitrate=4426.1kbits/s
    5596 speed=3.06x frame= 230 fps=152 q=25.0 size= 6025kB time=00:00:06.04
    5597 bitrate=8171.4kbits/s speed=3.99x frame= 317 fps=157 q=25.0 size= 12658kB
    5598 time=00:00:09.52 bitrate=10891.7kbits/s speed=4.73x frame= 404 fps=161 q=25.0
    5599 size= 18823kB time=00:00:13.00 bitrate=11861.3kbits/s speed=5.17x frame= 482
    5600 fps=160 q=25.0 size= 24254kB time=00:00:16.12 bitrate=12325.6kbits/s
    5601 speed=5.35x frame= 569 fps=162 q=25.0 size= 30513kB time=00:00:19.60
    5602 bitrate=12753.0kbits/s speed=5.57x frame= 656 fps=162 q=25.0 size= 36817kB
    5603 time=00:00:23.08 bitrate=13067.8kbits/s speed= 5.7x frame= 744 fps=164 q=25.0
    5604 size= 43111kB time=00:00:26.60 bitrate=13276.7kbits/s speed=5.85x frame= 833
    5605 fps=165 q=25.0 size= 49483kB time=00:00:30.16 bitrate=13440.4kbits/s
    5606 speed=5.97x frame= 917 fps=165 q=25.0 size= 55575kB time=00:00:33.52
    5607 bitrate=13582.0kbits/s speed=6.04x frame= 1006 fps=166 q=25.0 size= 61701kB
    5608 time=00:00:37.08 bitrate=13631.5kbits/s speed=6.12x frame= 1091 fps=166 q=25.0
    5609 size= 67214kB time=00:00:40.48 bitrate=13602.1kbits/s speed=6.17x frame= 1180
    5610 fps=167 q=25.0 size= 72771kB time=00:00:44.04 bitrate=13536.4kbits/s
    5611 speed=6.24x frame= 1269 fps=168 q=25.0 size= 78098kB time=00:00:47.60
    5612 bitrate=13440.7kbits/s speed=6.29x frame= 1353 fps=168 q=25.0 size= 82790kB
    5613 time=00:00:50.96 bitrate=13308.7kbits/s speed=6.32x frame= 1442 fps=168 q=25.0
    5614 size= 87426kB time=00:00:54.52 bitrate=13136.4kbits/s speed=6.36x frame= 1532
    5615 fps=169 q=25.0 size= 91864kB time=00:00:58.12 bitrate=12948.3kbits/s speed=
    5616 6.4x frame= 1617 fps=169 q=25.0 size= 95915kB time=00:01:01.52
    5617 bitrate=12772.1kbits/s speed=6.42x frame= 1706 fps=169 q=25.0 size= 99937kB
    5618 time=00:01:05.08 bitrate=12579.7kbits/s speed=6.45x frame= 1795 fps=170 q=25.0
    5619 size= 103922kB time=00:01:08.64 bitrate=12402.8kbits/s speed=6.48x frame= 1878
    5620 fps=169 q=25.0 size= 107590kB time=00:01:11.96 bitrate=12248.1kbits/s
    5621 speed=6.49x frame= 1966 fps=170 q=25.0 size= 110849kB time=00:01:15.48
    5622 bitrate=12030.7kbits/s speed=6.51x frame= 2054 fps=170 q=25.0 size= 116186kB
    5623 time=00:01:19.00 bitrate=12048.1kbits/s speed=6.53x frame= 2142 fps=170 q=25.0
    5624 size= 121307kB time=00:01:22.52 bitrate=12042.5kbits/s speed=6.55x frame= 2230
    5625 fps=170 q=25.0 size= 127266kB time=00:01:26.04 bitrate=12117.2kbits/s
    5626 speed=6.57x frame= 2318 fps=170 q=25.0 size= 131561kB time=00:01:29.56
    5627 bitrate=12033.8kbits/s speed=6.59x frame= 2405 fps=171 q=25.0 size= 134057kB
    5628 time=00:01:33.04 bitrate=11803.4kbits/s speed= 6.6x frame= 2494 fps=171 q=25.0
    5629 size= 135297kB time=00:01:36.60 bitrate=11473.6kbits/s speed=6.62x frame= 2584
    5630 fps=171 q=25.0 size= 136340kB time=00:01:40.20 bitrate=11146.7kbits/s
    5631 speed=6.63x frame= 2667 fps=171 q=25.0 size= 137370kB time=00:01:43.52
    5632 bitrate=10870.7kbits/s speed=6.63x frame= 2749 fps=171 q=25.0 size= 138613kB
    5633 time=00:01:46.80 bitrate=10632.2kbits/s speed=6.63x frame= 2830 fps=170 q=25.0
    5634 size= 139607kB time=00:01:50.04 bitrate=10393.1kbits/s speed=6.62x frame= 2910
    5635 fps=170 q=25.0 size= 140624kB time=00:01:53.24 bitrate=10173.0kbits/s
    5636 speed=6.61x frame= 2994 fps=170 q=25.0 size= 141666kB time=00:01:56.60
    5637 bitrate=9953.0kbits/s speed=6.61x frame= 3078 fps=170 q=25.0 size= 142646kB
    5638 time=00:01:59.96 bitrate=9741.2kbits/s speed=6.62x frame= 3167 fps=170 q=25.0
    5639 size= 143594kB time=00:02:03.52 bitrate=9523.3kbits/s speed=6.63x frame= 3254
    5640 fps=170 q=25.0 size= 144663kB time=00:02:07.00 bitrate=9331.4kbits/s
    5641 speed=6.64x frame= 3345 fps=170 q=25.0 size= 145501kB time=00:02:10.64
    5642 bitrate=9123.9kbits/s speed=6.65x frame= 3436 fps=171 q=25.0 size= 146505kB
    5643 time=00:02:14.28 bitrate=8937.8kbits/s speed=6.67x frame= 3527 fps=171 q=25.0
    5644 size= 147412kB time=00:02:17.92 bitrate=8755.8kbits/s speed=6.68x frame= 3618
    5645 fps=171 q=25.0 size= 148221kB time=00:02:21.56 bitrate=8577.5kbits/s
    5646 speed=6.69x frame= 3709 fps=171 q=25.0 size= 149054kB time=00:02:25.20
    5647 bitrate=8409.4kbits/s speed=6.71x frame= 3800 fps=172 q=25.0 size= 149760kB
    5648 time=00:02:28.84 bitrate=8242.7kbits/s speed=6.72x frame= 3891 fps=172 q=25.0
    5649 size= 150377kB time=00:02:32.48 bitrate=8079.0kbits/s speed=6.73x frame= 3982
    5650 fps=172 q=25.0 size= 151132kB time=00:02:36.12 bitrate=7930.3kbits/s
    5651 speed=6.74x frame= 4029 fps=171 q=-1.0 Lsize= 152060kB time=00:02:41.04
    5652 bitrate=7735.2kbits/s speed=6.85x 
    5653 video:152015kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
    5654 muxing overhead: 0.029385% 
    5655 [libx264 @ 0x2f41260] frame I:18 Avg QP:11.68 size:146649 
    5656 [libx264 @ 0x2f41260] frame P:1617 Avg QP:18.50 size: 44842 
    5657 [libx264 @ 0x2f41260] frame B:2394 Avg QP:23.32 size: 33631 
    5658 [libx264 @ 0x2f41260] consecutive B-frames: 16.9% 7.5% 12.4% 63.1% 
    5659 [libx264 @ 0x2f41260] mb I I16..4: 52.0% 30.2% 17.8% 
    5660 [libx264 @ 0x2f41260] mb P I16..4: 1.1% 3.0% 1.6% P16..4: 7.9% 4.3% 4.4% 0.0%
    5661 0.0% skip:77.7% 
    5662 [libx264 @ 0x2f41260] mb B I16..4: 0.3% 1.2% 0.6% B16..8: 9.2% 3.0% 1.5%
    5663 direct: 5.0% skip:79.1% L0:34.0% L1:38.4% BI:27.6% 
    5664 [libx264 @ 0x2f41260] 8x8 transform intra:51.8% inter:33.7% 
    5665 [libx264 @ 0x2f41260] coded y,uvDC,uvAC intra: 70.6% 35.1% 31.0% inter: 10.9%
    5666 6.3% 4.1% 
    5667 [libx264 @ 0x2f41260] i16 v,h,dc,p: 68% 29% 3% 1% 
    5668 [libx264 @ 0x2f41260] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 6% 39% 7% 7% 9% 5% 8%
    5669 7% 
    5670 [libx264 @ 0x2f41260] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 9% 20% 9% 9% 12% 8%
    5671 10% 8% 
    5672 [libx264 @ 0x2f41260] i8c dc,h,v,p: 70% 13% 16% 2% 
    5673 [libx264 @ 0x2f41260] Weighted P-Frames: Y:0.1% UV:0.1% 
    5674 [libx264 @ 0x2f41260] ref P L0: 72.3% 12.7% 9.9% 5.1% 0.0% 
    5675 [libx264 @ 0x2f41260] ref B L0: 89.2% 8.1% 2.6% 
    5676 [libx264 @ 0x2f41260] ref B L1: 97.6% 2.4% 
    5677 [libx264 @ 0x2f41260] kb/s:7727.11 
    5678  
    5679 Movie saved to /tmp/imprima/.../movies/F107-A3_full_bin2_srv.mp4 
    5680  
    5681 executed F107-A3_session.cxc 
    5682 
    5683 > close session
    5684 
    5685 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    5686 
    5687 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5688 step 1, values int8 
    5689 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5690 shown at step 1, values int8 
    5691 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5692 shown at step 1, values int8 
    5693 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5694 shown at step 1, values int8 
    5695 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5696 shown at step 1, values int8 
    5697 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    5698 © 2016-2022 Regents of the University of California. All rights reserved. 
    5699 How to cite UCSF ChimeraX 
    5700 
    5701 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5702 
    5703 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5704 step 2, values int8 
    5705 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5706 shown at level 0.8, step 2, values int8 
    5707 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5708 shown at level 0.8, step 3, values int8 
    5709 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5710 shown at level 0.8, step 2, values int8 
    5711 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5712 shown at level 0.8, step 2, values int8 
    5713 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    5714 the model panel to edit those fields 
    5715 UCSF ChimeraX version: 1.4 (2022-06-03) 
    5716 © 2016-2022 Regents of the University of California. All rights reserved. 
    5717 How to cite UCSF ChimeraX 
    5718 
    5719 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    5720 
    5721 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5722 step 1, values int8 
    5723 
    5724 > volume showOutlineBox true
    5725 
    5726 > volume region all imageMode "full region"
    5727 
    5728 > volume unzone
    5729 
    5730 > mousemode rightMode "crop volume"
    5731 
    5732 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    5733 > "box faces"
    5734 
    5735 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5736 
    5737 > volume #1 region 0,0,0,1385,1409,1604
    5738 
    5739 > volume #1 region all
    5740 
    5741 > volume #1 region 0,0,0,2129,1523,1748
    5742 
    5743 > view orient
    5744 
    5745 > zoom 0.85
    5746 
    5747 > view name p1
    5748 
    5749 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5750 
    5751 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5752 shown at step 1, values int8 
    5753 
    5754 > close #2
    5755 
    5756 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    5757 
    5758 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5759 shown at step 1, values int8 
    5760 
    5761 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    5762 
    5763 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5764 shown at step 1, values int8 
    5765 
    5766 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    5767 
    5768 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5769 shown at step 1, values int8 
    5770 
    5771 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    5772 
    5773 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5774 shown at step 1, values int8 
    5775 
    5776 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5777 
    5778 > volume #2 show style surface level 0.8 color #5555ff
    5779 
    5780 > volume #1 region 0,0,0,2129,1523,1740
    5781 
    5782 > volume all region 0,0,0,2129,1523,1740
    5783 
    5784 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5785 > showOutlineBox true imageMode "box faces"
    5786 
    5787 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5788 > showOutlineBox true imageMode "box faces"
    5789 
    5790 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    5791 > showOutlineBox true imageMode "box faces"
    5792 
    5793 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    5794 > faces"
    5795 
    5796 > volume #2 show style surface level -50 color #5555ff
    5797 
    5798 > volume #2 show style surface level 10 color #5555ff
    5799 
    5800 > lighting soft
    5801 
    5802 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5803 
    5804 > volume #2 show style surface level 0.8 color #5555ff
    5805 
    5806 > volume #3 show style surface level 0.8 color #aa557f
    5807 
    5808 > volume #4 show style surface level 0.8 color #f514fd
    5809 
    5810 > volume #5 show style surface level 0.8 color #11ffcc
    5811 
    5812 > ~display #1
    5813 
    5814 > volume #2 transparency 0.6
    5815 
    5816 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5817 
    5818 > display #1
    5819 
    5820 > volume all region 0,0,0,2129,1523,1744
    5821 
    5822 > ~display #1
    5823 
    5824 > volume #2 show style surface step 2
    5825 
    5826 > volume #3 show style surface step 3
    5827 
    5828 > volume #4 show style surface step 2
    5829 
    5830 > volume #5 show style surface step 2
    5831 
    5832 > volume #5 show style surface step 1
    5833 
    5834 > volume #5 show style surface step 2
    5835 
    5836 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5837 
    5838 > view name p2
    5839 
    5840 > view list
    5841 
    5842 Named views: p1, p2 
    5843 
    5844 > view p1
    5845 
    5846 > view p2
    5847 
    5848 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5849 
    5850 > fly p2 p1 100
    5851 
    5852 > wait
    5853 
    5854 > view p2
    5855 
    5856 > display #1
    5857 
    5858 > volume #1 region 0,0,0,2129,1523,1744
    5859 
    5860 > volume #1 region 0,0,0,2129,1523,1740
    5861 
    5862 > volume #1 region 0,0,0,2129,1523,1742
    5863 
    5864 > volume #1 region 0,0,0,2129,1523,1743
    5865 
    5866 > volume #1 region 0,0,0,2129,1523,1744
    5867 
    5868 > volume #1 region 0,0,0,2129,1523,1743
    5869 
    5870 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5871 
    5872 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    5873 
    5874 opened ChimeraX session 
    5875 
    5876 > display #1
    5877 
    5878 > ~display #2-5
    5879 
    5880 > display #2-5
    5881 
    5882 > ~display #1
    5883 
    5884 > display #1
    5885 
    5886 > ~display #2-5
    5887 
    5888 > volume all region 0,0,0,2129,1523,1743
    5889 
    5890 > display #2-5
    5891 
    5892 > view p2
    5893 
    5894 > lighting soft
    5895 
    5896 > view p1
    5897 
    5898 > help hide
    5899 
    5900 > hide #1
    5901 
    5902 > view p2
    5903 
    5904 > show #2
    5905 
    5906 > volume #2-5 show style surface
    5907 
    5908 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5909 
    5910 > display #1
    5911 
    5912 > ~display #2-5
    5913 
    5914 > volume #2-5 show style surface
    5915 
    5916 > ~display #2-5
    5917 
    5918 > fly p2 p1 100
    5919 
    5920 > wait
    5921 
    5922 > volume #2-5 show style surface transparency 0.5
    5923 
    5924 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    5925 > bgColor black margin 5
    5926 
    5927 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    5928 > bgColor black margin 5
    5929 
    5930 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    5931 > true bgColor black margin 5
    5932 
    5933 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    5934 > true bgColor black margin 5
    5935 
    5936 > volume all planes z,1743,30
    5937 
    5938 > wait 1700
    5939 
    5940 > close session
    5941 
    5942 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    5943 
    5944 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5945 step 1, values int8 
    5946 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5947 shown at level 0.8, step 1, values int8 
    5948 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5949 shown at level 0.8, step 1, values int8 
    5950 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5951 shown at level 0.8, step 1, values int8 
    5952 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5953 shown at level 0.8, step 1, values int8 
    5954 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    5955 © 2016-2022 Regents of the University of California. All rights reserved. 
    5956 How to cite UCSF ChimeraX 
    5957 
    5958 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5959 
    5960 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5961 step 2, values int8 
    5962 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    5963 shown at level 0.8, step 2, values int8 
    5964 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    5965 shown at level 0.8, step 3, values int8 
    5966 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    5967 shown at level 0.8, step 2, values int8 
    5968 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    5969 shown at level 0.8, step 2, values int8 
    5970 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    5971 the model panel to edit those fields 
    5972 UCSF ChimeraX version: 1.4 (2022-06-03) 
    5973 © 2016-2022 Regents of the University of California. All rights reserved. 
    5974 How to cite UCSF ChimeraX 
    5975 
    5976 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    5977 
    5978 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    5979 step 1, values int8 
    5980 
    5981 > volume showOutlineBox true
    5982 
    5983 > volume region all imageMode "full region"
    5984 
    5985 > volume unzone
    5986 
    5987 > mousemode rightMode "crop volume"
    5988 
    5989 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    5990 > "box faces"
    5991 
    5992 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    5993 
    5994 > volume #1 region 0,0,0,1385,1409,1604
    5995 
    5996 > volume #1 region all
    5997 
    5998 > volume #1 region 0,0,0,2129,1523,1748
    5999 
    6000 > view orient
    6001 
    6002 > zoom 0.85
    6003 
    6004 > view name p1
    6005 
    6006 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    6007 
    6008 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6009 shown at step 1, values int8 
    6010 
    6011 > close #2
    6012 
    6013 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    6014 
    6015 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6016 shown at step 1, values int8 
    6017 
    6018 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    6019 
    6020 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    6021 shown at step 1, values int8 
    6022 
    6023 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    6024 
    6025 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    6026 shown at step 1, values int8 
    6027 
    6028 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    6029 
    6030 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    6031 shown at step 1, values int8 
    6032 
    6033 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6034 
    6035 > volume #2 show style surface level 0.8 color #5555ff
    6036 
    6037 > volume #1 region 0,0,0,2129,1523,1740
    6038 
    6039 > volume all region 0,0,0,2129,1523,1740
    6040 
    6041 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6042 > showOutlineBox true imageMode "box faces"
    6043 
    6044 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6045 > showOutlineBox true imageMode "box faces"
    6046 
    6047 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6048 > showOutlineBox true imageMode "box faces"
    6049 
    6050 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    6051 > faces"
    6052 
    6053 > volume #2 show style surface level -50 color #5555ff
    6054 
    6055 > volume #2 show style surface level 10 color #5555ff
    6056 
    6057 > lighting soft
    6058 
    6059 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6060 
    6061 > volume #2 show style surface level 0.8 color #5555ff
    6062 
    6063 > volume #3 show style surface level 0.8 color #aa557f
    6064 
    6065 > volume #4 show style surface level 0.8 color #f514fd
    6066 
    6067 > volume #5 show style surface level 0.8 color #11ffcc
    6068 
    6069 > ~display #1
    6070 
    6071 > volume #2 transparency 0.6
    6072 
    6073 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6074 
    6075 > display #1
    6076 
    6077 > volume all region 0,0,0,2129,1523,1744
    6078 
    6079 > ~display #1
    6080 
    6081 > volume #2 show style surface step 2
    6082 
    6083 > volume #3 show style surface step 3
    6084 
    6085 > volume #4 show style surface step 2
    6086 
    6087 > volume #5 show style surface step 2
    6088 
    6089 > volume #5 show style surface step 1
    6090 
    6091 > volume #5 show style surface step 2
    6092 
    6093 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6094 
    6095 > view name p2
    6096 
    6097 > view list
    6098 
    6099 Named views: p1, p2 
    6100 
    6101 > view p1
    6102 
    6103 > view p2
    6104 
    6105 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6106 
    6107 > fly p2 p1 100
    6108 
    6109 > wait
    6110 
    6111 > view p2
    6112 
    6113 > display #1
    6114 
    6115 > volume #1 region 0,0,0,2129,1523,1744
    6116 
    6117 > volume #1 region 0,0,0,2129,1523,1740
    6118 
    6119 > volume #1 region 0,0,0,2129,1523,1742
    6120 
    6121 > volume #1 region 0,0,0,2129,1523,1743
    6122 
    6123 > volume #1 region 0,0,0,2129,1523,1744
    6124 
    6125 > volume #1 region 0,0,0,2129,1523,1743
    6126 
    6127 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6128 
    6129 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    6130 
    6131 opened ChimeraX session 
    6132 
    6133 > display #1
    6134 
    6135 > ~display #2-5
    6136 
    6137 > display #2-5
    6138 
    6139 > ~display #1
    6140 
    6141 > display #1
    6142 
    6143 > ~display #2-5
    6144 
    6145 > volume all region 0,0,0,2129,1523,1743
    6146 
    6147 > display #2-5
    6148 
    6149 > view p2
    6150 
    6151 > lighting soft
    6152 
    6153 > view p1
    6154 
    6155 > help hide
    6156 
    6157 > hide #1
    6158 
    6159 > view p2
    6160 
    6161 > show #2
    6162 
    6163 > volume #2-5 show style surface
    6164 
    6165 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6166 
    6167 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    6168 
    6169 opened ChimeraX session 
    6170 
    6171 > display #1
    6172 
    6173 > ~display #2-5
    6174 
    6175 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6176 
    6177 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    6178 
    6179 opened ChimeraX session 
    6180 
    6181 > view orient
    6182 
    6183 > close session
    6184 
    6185 > open /tmp/imprima/F107A1_bin2/data/f107a_flipz.mrc
    6186 
    6187 Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
    6188 step 1, values int8 
    6189 
    6190 > save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
    6191 
    6192 > volume showOutlineBox true
    6193 
    6194 > volume #1 region 0,0,0,1646,1505,1349 step 8
    6195 
    6196 > volume #1 region 0,0,0,1646,1505,1349 step 1 colorMode opaque8 imageMode
    6197 > "box faces"
    6198 
    6199 > view orient
    6200 
    6201 > view name p1
    6202 
    6203 > view list
    6204 
    6205 Named views: p1 
    6206 
    6207 > save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
    6208 
    6209 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6210 
    6211 > view name p2
    6212 
    6213 > ui mousemode right "crop volume"
    6214 
    6215 > volume #1 region 0,0,0,1646,1505,1094
    6216 
    6217 > view p1
    6218 
    6219 > volume #1 region 0,0,0,1646,1505,1349
    6220 
    6221 > volume #1 planes z,1349,1094
    6222 
    6223 > wait 255
    6224 
    6225 > wait
    6226 
    6227 wait requires a frame count argument unless motion is in progress 
    6228 
    6229 > volume #1 region 0,0,0,1646,1505,1349
    6230 
    6231 > volume #1 planes z,1349,1094
    6232 
    6233 > wait 255
    6234 
    6235 > volume #1 region 0,0,0,1646,1505,1349
    6236 
    6237 > volume #1 planes z,1349,1300
    6238 
    6239 > wait 50
    6240 
    6241 > help 2dlabels
    6242 
    6243 [Repeated 1 time(s)]
    6244 
    6245 > volume #1 region 0,0,0,1646,1505,1349
    6246 
    6247 > volume #1 planes z,1349,1300
    6248 
    6249 > wait 50
    6250 
    6251 > volume #1 region 0,0,0,1646,1505,1349
    6252 
    6253 > 2dlabels arrow #7.1 start 0.083,0.643 end 0.357,0.413 color red weight 0.7
    6254 > headStyle solid
    6255 
    6256 No 2D arrows in session 
    6257 
    6258 > 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.7
    6259 > headStyle solid
    6260 
    6261 > volume #1 region 0,0,0,1646,1505,1349
    6262 
    6263 > view p1
    6264 
    6265 > ui mousemode right "move label"
    6266 
    6267 > 2dlabels arrow #2.1 end 0.363,0.765
    6268 
    6269 > 2dlabels arrow #2.1 start 0.112,0.919
    6270 
    6271 > 2dlabels arrow #2.1 start 0.112,0.919 end 0.363,0.765 color white
    6272 
    6273 > 2dlabels arrow start 0.112,0.819 end 0.363,0.765 color white
    6274 
    6275 > 2dlabels arrow #2.1 end 0.362,0.785
    6276 
    6277 > 2dlabels arrow #2.2 end 0.343,0.523
    6278 
    6279 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white
    6280 
    6281 > help 2dlabels
    6282 
    6283 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white bold false
    6284 
    6285 Expected a keyword 
    6286 
    6287 > help 2dlabels
    6288 
    6289 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 bold false color white
    6290 
    6291 Expected ',' or a keyword 
    6292 
    6293 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white, bold
    6294 > false
    6295 
    6296 Invalid "color" argument: Expected 'default' or a color 
    6297 
    6298 > view p1
    6299 
    6300 > help 2dlabels
    6301 
    6302 > 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white weight 0.5
    6303 
    6304 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6305 > margin 5 visibility true
    6306 
    6307 > 2dlabels arrow #2.1 weight 0.5
    6308 
    6309 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6310 
    6311 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6312 > margin 5 visibility true
    6313 
    6314 > 2dlabels arrow #2.1 end 0.362,0.784
    6315 
    6316 > 2dlabels arrow #2.1 start 0.112,0.916
    6317 
    6318 > 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.5
    6319 > headStyle solid
    6320 
    6321 > 2dlabels arrow #2.3 start 0.830,0.911
    6322 
    6323 > 2dlabels arrow #2.3 end 0.580,0.728
    6324 
    6325 > 2dlabels arrow #2.3 start 0.824,0.922
    6326 
    6327 > 2dlabels arrow #2.3 start 0.824,0.922 end 0.580,0.728 color white
    6328 
    6329 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6330 
    6331 > 2dlabels arrow start 0.824,0.922 end 0.780,0.928 color white
    6332 
    6333 > 2dlabels arrow #2.4 end 0.652,0.427
    6334 
    6335 > 2dlabels arrow #2.3 start 0.813,0.939
    6336 
    6337 > 2dlabels arrow #2.4 start 0.851,0.886
    6338 
    6339 > 2dlabels arrow #2.4 weight 0.5
    6340 
    6341 > 2dlabels arrow #2.4 weight 0.5 headStyle solid
    6342 
    6343 > 2dlabels arrow #2.4 end 0.655,0.424
    6344 
    6345 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6346 
    6347 > volume #1 region 0,0,0,1646,1505,1349
    6348 
    6349 [Repeated 1 time(s)]
    6350 
    6351 > volume #1 region 0,0,0,1646,1505,1300
    6352 
    6353 > 2dlabels arrow #2.1 end 0.442,0.807
    6354 
    6355 > 2dlabels arrow #2.2 end 0.331,0.561
    6356 
    6357 > 2dlabels arrow #2.3 end 0.591,0.756
    6358 
    6359 > 2dlabels arrow #2.4 end 0.662,0.510
    6360 
    6361 > volume #1 region 0,0,0,1646,1505,1349
    6362 
    6363 > help 2dlabels\
    6364 
    6365 No help found for '2dlabels\' 
    6366 
    6367 > help 2dlabels
    6368 
    6369 > 2dlabels #all visbility false
    6370 
    6371 Expected 'all' or a 2d label name or a label models specifier or a keyword 
    6372 
    6373 > 2dlabels all visbility false
    6374 
    6375 Expected a keyword 
    6376 
    6377 > 2dlabels all visibility false
    6378 
    6379 > 2dlabels arrow all visibility false
    6380 
    6381 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6382 
    6383 > volume #1 region 0,0,0,1646,1505,1300
    6384 
    6385 > volume #1 region 0,0,0,1646,1300,1000 wait 100;
    6386 
    6387 Expected a keyword 
    6388 
    6389 > volume #1 region 0,0,0,1646,1300,1000
    6390 
    6391 > wait 100
    6392 
    6393 > volume #1 region 0,0,0,1646,1505,1349
    6394 
    6395 > volume #1 planes z,1349,1300
    6396 
    6397 > wait 50
    6398 
    6399 > volume #1 planes z,1300,1000
    6400 
    6401 > wait 101
    6402 
    6403 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6404 
    6405 > volume #1 region 0,0,0,1646,1505,1349
    6406 
    6407 > save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
    6408 
    6409 ——— End of log from Fri Jul 29 13:26:07 2022 ———
    6410 
    6411 opened ChimeraX session 
    6412 
    6413 > close #2-3
    6414 
    6415 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6416 > margin 5 visibility true
    6417 
    6418 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6419 > margin 5 visibility true
    6420 
    6421 > 2dlabels text #3.3 "Microvilli" size 18 xpos .03 ypos .42 bold true bgColor
    6422 > black margin 5 visibility true;
    6423 
    6424 Expected a keyword 
    6425 
    6426 > 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
    6427 > margin 5 visibility true
    6428 
    6429 > 2dlabels text prova size 18 xpos .03 ypos .62 bold true bgColor black margin
    6430 > 5 visibility true
    6431 
    6432 > close #2.4
    6433 
    6434 > 2dlabels text prova size 18 xpos .03 ypos .62 bold true bgColor black margin
    6435 > 5 visibility false
    6436 
    6437 > close #2.4
    6438 
    6439 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6440 > visibility true
    6441 
    6442 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6443 > visibility true
    6444 
    6445 > 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
    6446 > visibility false
    6447 
    6448 > 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
    6449 > visibility false
    6450 
    6451 > hide #2.1 models
    6452 
    6453 > hide #2.2 models
    6454 
    6455 > hide #2.3 models
    6456 
    6457 > hide #3.1 models
    6458 
    6459 > hide #3.2 models
    6460 
    6461 > hide #3.3 models
    6462 
    6463 > hide #3.4 models
    6464 
    6465 > show #2.1 models
    6466 
    6467 > show #2.2 models
    6468 
    6469 > show #3.1 models
    6470 
    6471 > show #3.2 models
    6472 
    6473 > show #3.3 models
    6474 
    6475 > show #3.4 models
    6476 
    6477 > close #2
    6478 
    6479 > close #3
    6480 
    6481 > volume #1 region 0,0,0,1646,1505,1349
    6482 
    6483 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations.cxc
    6484 
    6485 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6486 > margin 5 visibility false
    6487 
    6488 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6489 > visibility false
    6490 
    6491 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6492 > visibility false
    6493 
    6494 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6495 > margin 5 visibility false
    6496 
    6497 > 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
    6498 > visibility false
    6499 
    6500 > 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
    6501 > visibility false
    6502 
    6503 > 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
    6504 > margin 5 visibility false
    6505 
    6506 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6507 > visibility false
    6508 
    6509 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6510 > visibility false
    6511 
    6512 > volume #1 planes z,1349,1300
    6513 
    6514 > wait 50
    6515 
    6516 > 2dlabels text #2.1-2 visibility true
    6517 
    6518 > 2dlabels arrow #3.1-4 visibility true
    6519 
    6520 No 2D arrows in session 
    6521 
    6522 > close #4
    6523 
    6524 > close #5
    6525 
    6526 > 2dlabels
    6527 
    6528 > 2dlabels help
    6529 
    6530 Expected 'all' or a 2d label name or a label models specifier or a keyword 
    6531 
    6532 > help 2dlabels
    6533 
    6534 > 2dlabels delete all
    6535 
    6536 > volume #1 region 0,0,0,1646,1505,1349
    6537 
    6538 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations.cxc
    6539 
    6540 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6541 > margin 5 visibility false
    6542 
    6543 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6544 > visibility false
    6545 
    6546 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6547 > visibility false
    6548 
    6549 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6550 > margin 5 visibility false
    6551 
    6552 > 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
    6553 > visibility false
    6554 
    6555 > 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
    6556 > visibility false
    6557 
    6558 > 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
    6559 > margin 5 visibility false
    6560 
    6561 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6562 > visibility false
    6563 
    6564 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6565 > visibility false
    6566 
    6567 > volume #1 planes z,1349,1300
    6568 
    6569 > wait 50
    6570 
    6571 > 2dlabels text #2.1-2 visibility true
    6572 
    6573 > 2dlabels arrow #3.1-4 visibility true
    6574 
    6575 No 2D arrows in session 
    6576 
    6577 > close #6
    6578 
    6579 > 2dlabels delete all
    6580 
    6581 Traceback (most recent call last): 
    6582 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6583 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    6584 cmd.run(cmd_text) 
    6585 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6586 packages/chimerax/core/commands/cli.py", line 2897, in run 
    6587 result = ci.function(session, **kw_args) 
    6588 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6589 packages/chimerax/label/label2d.py", line 280, in label_delete 
    6590 l.delete() 
    6591 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6592 packages/chimerax/label/arrows.py", line 414, in delete 
    6593 lm.delete_arrow(self) 
    6594 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6595 packages/chimerax/label/arrows.py", line 312, in delete_arrow 
    6596 del self._named_arrows[arrow.name] 
    6597 KeyError: 'arrow 1' 
    6598  
    6599 KeyError: 'arrow 1' 
    6600  
    6601 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6602 packages/chimerax/label/arrows.py", line 312, in delete_arrow 
    6603 del self._named_arrows[arrow.name] 
    6604  
    6605 See log for complete Python traceback. 
    6606  
    6607 
    6608 > close #7
    6609 
    6610 > 2dlabels delete all
    6611 
    6612 > volume #1 region 0,0,0,1646,1505,1349
    6613 
    6614 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations.cxc
    6615 
    6616 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6617 > margin 5 visibility false
    6618 
    6619 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6620 > visibility false
    6621 
    6622 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6623 > visibility false
    6624 
    6625 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6626 > margin 5 visibility false
    6627 
    6628 > 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
    6629 > visibility false
    6630 
    6631 > 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
    6632 > visibility false
    6633 
    6634 > 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
    6635 > margin 5 visibility false
    6636 
    6637 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6638 > visibility false
    6639 
    6640 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6641 > visibility false
    6642 
    6643 > volume #1 planes z,1349,1300
    6644 
    6645 > wait 50
    6646 
    6647 > 2dlabels text #2.1-2 visibility true frames 200
    6648 
    6649 > 2dlabels arrow #3.1-4 visibility true frames 200
    6650 
    6651 No 2D arrows in session 
    6652 
    6653 > volume #1 region 0,0,0,1646,1505,1349
    6654 
    6655 > 2dlabels delete all
    6656 
    6657 Traceback (most recent call last): 
    6658 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6659 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    6660 cmd.run(cmd_text) 
    6661 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6662 packages/chimerax/core/commands/cli.py", line 2897, in run 
    6663 result = ci.function(session, **kw_args) 
    6664 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6665 packages/chimerax/label/label2d.py", line 280, in label_delete 
    6666 l.delete() 
    6667 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6668 packages/chimerax/label/arrows.py", line 414, in delete 
    6669 lm.delete_arrow(self) 
    6670 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6671 packages/chimerax/label/arrows.py", line 312, in delete_arrow 
    6672 del self._named_arrows[arrow.name] 
    6673 KeyError: 'arrow 1' 
    6674  
    6675 KeyError: 'arrow 1' 
    6676  
    6677 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
    6678 packages/chimerax/label/arrows.py", line 312, in delete_arrow 
    6679 del self._named_arrows[arrow.name] 
    6680  
    6681 See log for complete Python traceback. 
    6682  
    6683 
    6684 > close #9
    6685 
    6686 > 2dlabels delete all
    6687 
    6688 > help 2dlab
    6689 
    6690 > open /tmp/imprima/F107A1_bin2/chimerax_flythrough_annotations.cxc
    6691 
    6692 > 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
    6693 > margin 5 visibility false
    6694 
    6695 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6696 > visibility false
    6697 
    6698 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6699 > visibility false
    6700 
    6701 > 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
    6702 > margin 5 visibility false
    6703 
    6704 > 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
    6705 > visibility false
    6706 
    6707 > 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
    6708 > visibility false
    6709 
    6710 > 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
    6711 > margin 5 visibility false
    6712 
    6713 > 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
    6714 > visibility false
    6715 
    6716 > 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
    6717 > visibility false
    6718 
    6719 > volume #1 planes z,1349,1300
    6720 
    6721 > wait 50
    6722 
    6723 > 2dlabels text #2.1-2 visibility true frames 200
    6724 
    6725 > 2dlabels arrow #3.1-4 visibility true frames 200
    6726 
    6727 No 2D arrows in session 
    6728 
    6729 > close session
    6730 
    6731 > open /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs format session
    6732 
    6733 Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
    6734 step 1, values int8 
    6735 Log from Fri Jul 29 13:26:07 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    6736 © 2016-2022 Regents of the University of California. All rights reserved. 
    6737 How to cite UCSF ChimeraX 
    6738 
    6739 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6740 
    6741 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    6742 step 1, values int8 
    6743 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6744 shown at step 1, values int8 
    6745 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    6746 shown at step 1, values int8 
    6747 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    6748 shown at step 1, values int8 
    6749 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    6750 shown at step 1, values int8 
    6751 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    6752 © 2016-2022 Regents of the University of California. All rights reserved. 
    6753 How to cite UCSF ChimeraX 
    6754 
    6755 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6756 
    6757 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    6758 step 2, values int8 
    6759 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6760 shown at level 0.8, step 2, values int8 
    6761 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    6762 shown at level 0.8, step 3, values int8 
    6763 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    6764 shown at level 0.8, step 2, values int8 
    6765 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    6766 shown at level 0.8, step 2, values int8 
    6767 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    6768 the model panel to edit those fields 
    6769 UCSF ChimeraX version: 1.4 (2022-06-03) 
    6770 © 2016-2022 Regents of the University of California. All rights reserved. 
    6771 How to cite UCSF ChimeraX 
    6772 
    6773 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    6774 
    6775 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    6776 step 1, values int8 
    6777 
    6778 > volume showOutlineBox true
    6779 
    6780 > volume region all imageMode "full region"
    6781 
    6782 > volume unzone
    6783 
    6784 > mousemode rightMode "crop volume"
    6785 
    6786 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    6787 > "box faces"
    6788 
    6789 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6790 
    6791 > volume #1 region 0,0,0,1385,1409,1604
    6792 
    6793 > volume #1 region all
    6794 
    6795 > volume #1 region 0,0,0,2129,1523,1748
    6796 
    6797 > view orient
    6798 
    6799 > zoom 0.85
    6800 
    6801 > view name p1
    6802 
    6803 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    6804 
    6805 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6806 shown at step 1, values int8 
    6807 
    6808 > close #2
    6809 
    6810 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    6811 
    6812 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    6813 shown at step 1, values int8 
    6814 
    6815 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    6816 
    6817 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    6818 shown at step 1, values int8 
    6819 
    6820 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    6821 
    6822 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    6823 shown at step 1, values int8 
    6824 
    6825 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    6826 
    6827 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    6828 shown at step 1, values int8 
    6829 
    6830 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6831 
    6832 > volume #2 show style surface level 0.8 color #5555ff
    6833 
    6834 > volume #1 region 0,0,0,2129,1523,1740
    6835 
    6836 > volume all region 0,0,0,2129,1523,1740
    6837 
    6838 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6839 > showOutlineBox true imageMode "box faces"
    6840 
    6841 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6842 > showOutlineBox true imageMode "box faces"
    6843 
    6844 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    6845 > showOutlineBox true imageMode "box faces"
    6846 
    6847 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    6848 > faces"
    6849 
    6850 > volume #2 show style surface level -50 color #5555ff
    6851 
    6852 > volume #2 show style surface level 10 color #5555ff
    6853 
    6854 > lighting soft
    6855 
    6856 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6857 
    6858 > volume #2 show style surface level 0.8 color #5555ff
    6859 
    6860 > volume #3 show style surface level 0.8 color #aa557f
    6861 
    6862 > volume #4 show style surface level 0.8 color #f514fd
    6863 
    6864 > volume #5 show style surface level 0.8 color #11ffcc
    6865 
    6866 > ~display #1
    6867 
    6868 > volume #2 transparency 0.6
    6869 
    6870 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6871 
    6872 > display #1
    6873 
    6874 > volume all region 0,0,0,2129,1523,1744
    6875 
    6876 > ~display #1
    6877 
    6878 > volume #2 show style surface step 2
    6879 
    6880 > volume #3 show style surface step 3
    6881 
    6882 > volume #4 show style surface step 2
    6883 
    6884 > volume #5 show style surface step 2
    6885 
    6886 > volume #5 show style surface step 1
    6887 
    6888 > volume #5 show style surface step 2
    6889 
    6890 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6891 
    6892 > view name p2
    6893 
    6894 > view list
    6895 
    6896 Named views: p1, p2 
    6897 
    6898 > view p1
    6899 
    6900 > view p2
    6901 
    6902 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6903 
    6904 > fly p2 p1 100
    6905 
    6906 > wait
    6907 
    6908 > view p2
    6909 
    6910 > display #1
    6911 
    6912 > volume #1 region 0,0,0,2129,1523,1744
    6913 
    6914 > volume #1 region 0,0,0,2129,1523,1740
    6915 
    6916 > volume #1 region 0,0,0,2129,1523,1742
    6917 
    6918 > volume #1 region 0,0,0,2129,1523,1743
    6919 
    6920 > volume #1 region 0,0,0,2129,1523,1744
    6921 
    6922 > volume #1 region 0,0,0,2129,1523,1743
    6923 
    6924 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6925 
    6926 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    6927 
    6928 opened ChimeraX session 
    6929 
    6930 > display #1
    6931 
    6932 > ~display #2-5
    6933 
    6934 > display #2-5
    6935 
    6936 > ~display #1
    6937 
    6938 > display #1
    6939 
    6940 > ~display #2-5
    6941 
    6942 > volume all region 0,0,0,2129,1523,1743
    6943 
    6944 > display #2-5
    6945 
    6946 > view p2
    6947 
    6948 > lighting soft
    6949 
    6950 > view p1
    6951 
    6952 > help hide
    6953 
    6954 > hide #1
    6955 
    6956 > view p2
    6957 
    6958 > show #2
    6959 
    6960 > volume #2-5 show style surface
    6961 
    6962 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    6963 
    6964 > display #1
    6965 
    6966 > ~display #2-5
    6967 
    6968 > volume #2-5 show style surface
    6969 
    6970 > ~display #2-5
    6971 
    6972 > fly p2 p1 100
    6973 
    6974 > wait
    6975 
    6976 > volume #2-5 show style surface transparency 0.5
    6977 
    6978 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    6979 > bgColor black margin 5
    6980 
    6981 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    6982 > bgColor black margin 5
    6983 
    6984 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    6985 > true bgColor black margin 5
    6986 
    6987 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    6988 > true bgColor black margin 5
    6989 
    6990 > volume all planes z,1743,30
    6991 
    6992 > wait 1700
    6993 
    6994 > close session
    6995 
    6996 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    6997 
    6998 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    6999 step 1, values int8 
    7000 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7001 shown at level 0.8, step 1, values int8 
    7002 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7003 shown at level 0.8, step 1, values int8 
    7004 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7005 shown at level 0.8, step 1, values int8 
    7006 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7007 shown at level 0.8, step 1, values int8 
    7008 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    7009 © 2016-2022 Regents of the University of California. All rights reserved. 
    7010 How to cite UCSF ChimeraX 
    7011 
    7012 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7013 
    7014 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7015 step 2, values int8 
    7016 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7017 shown at level 0.8, step 2, values int8 
    7018 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7019 shown at level 0.8, step 3, values int8 
    7020 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7021 shown at level 0.8, step 2, values int8 
    7022 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7023 shown at level 0.8, step 2, values int8 
    7024 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    7025 the model panel to edit those fields 
    7026 UCSF ChimeraX version: 1.4 (2022-06-03) 
    7027 © 2016-2022 Regents of the University of California. All rights reserved. 
    7028 How to cite UCSF ChimeraX 
    7029 
    7030 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    7031 
    7032 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7033 step 1, values int8 
    7034 
    7035 > volume showOutlineBox true
    7036 
    7037 > volume region all imageMode "full region"
    7038 
    7039 > volume unzone
    7040 
    7041 > mousemode rightMode "crop volume"
    7042 
    7043 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    7044 > "box faces"
    7045 
    7046 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7047 
    7048 > volume #1 region 0,0,0,1385,1409,1604
    7049 
    7050 > volume #1 region all
    7051 
    7052 > volume #1 region 0,0,0,2129,1523,1748
    7053 
    7054 > view orient
    7055 
    7056 > zoom 0.85
    7057 
    7058 > view name p1
    7059 
    7060 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7061 
    7062 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7063 shown at step 1, values int8 
    7064 
    7065 > close #2
    7066 
    7067 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    7068 
    7069 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7070 shown at step 1, values int8 
    7071 
    7072 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    7073 
    7074 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7075 shown at step 1, values int8 
    7076 
    7077 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7078 
    7079 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7080 shown at step 1, values int8 
    7081 
    7082 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    7083 
    7084 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7085 shown at step 1, values int8 
    7086 
    7087 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7088 
    7089 > volume #2 show style surface level 0.8 color #5555ff
    7090 
    7091 > volume #1 region 0,0,0,2129,1523,1740
    7092 
    7093 > volume all region 0,0,0,2129,1523,1740
    7094 
    7095 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7096 > showOutlineBox true imageMode "box faces"
    7097 
    7098 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7099 > showOutlineBox true imageMode "box faces"
    7100 
    7101 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7102 > showOutlineBox true imageMode "box faces"
    7103 
    7104 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    7105 > faces"
    7106 
    7107 > volume #2 show style surface level -50 color #5555ff
    7108 
    7109 > volume #2 show style surface level 10 color #5555ff
    7110 
    7111 > lighting soft
    7112 
    7113 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7114 
    7115 > volume #2 show style surface level 0.8 color #5555ff
    7116 
    7117 > volume #3 show style surface level 0.8 color #aa557f
    7118 
    7119 > volume #4 show style surface level 0.8 color #f514fd
    7120 
    7121 > volume #5 show style surface level 0.8 color #11ffcc
    7122 
    7123 > ~display #1
    7124 
    7125 > volume #2 transparency 0.6
    7126 
    7127 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7128 
    7129 > display #1
    7130 
    7131 > volume all region 0,0,0,2129,1523,1744
    7132 
    7133 > ~display #1
    7134 
    7135 > volume #2 show style surface step 2
    7136 
    7137 > volume #3 show style surface step 3
    7138 
    7139 > volume #4 show style surface step 2
    7140 
    7141 > volume #5 show style surface step 2
    7142 
    7143 > volume #5 show style surface step 1
    7144 
    7145 > volume #5 show style surface step 2
    7146 
    7147 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7148 
    7149 > view name p2
    7150 
    7151 > view list
    7152 
    7153 Named views: p1, p2 
    7154 
    7155 > view p1
    7156 
    7157 > view p2
    7158 
    7159 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7160 
    7161 > fly p2 p1 100
    7162 
    7163 > wait
    7164 
    7165 > view p2
    7166 
    7167 > display #1
    7168 
    7169 > volume #1 region 0,0,0,2129,1523,1744
    7170 
    7171 > volume #1 region 0,0,0,2129,1523,1740
    7172 
    7173 > volume #1 region 0,0,0,2129,1523,1742
    7174 
    7175 > volume #1 region 0,0,0,2129,1523,1743
    7176 
    7177 > volume #1 region 0,0,0,2129,1523,1744
    7178 
    7179 > volume #1 region 0,0,0,2129,1523,1743
    7180 
    7181 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7182 
    7183 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    7184 
    7185 opened ChimeraX session 
    7186 
    7187 > display #1
    7188 
    7189 > ~display #2-5
    7190 
    7191 > display #2-5
    7192 
    7193 > ~display #1
    7194 
    7195 > display #1
    7196 
    7197 > ~display #2-5
    7198 
    7199 > volume all region 0,0,0,2129,1523,1743
    7200 
    7201 > display #2-5
    7202 
    7203 > view p2
    7204 
    7205 > lighting soft
    7206 
    7207 > view p1
    7208 
    7209 > help hide
    7210 
    7211 > hide #1
    7212 
    7213 > view p2
    7214 
    7215 > show #2
    7216 
    7217 > volume #2-5 show style surface
    7218 
    7219 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7220 
    7221 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    7222 
    7223 opened ChimeraX session 
    7224 
    7225 > display #1
    7226 
    7227 > ~display #2-5
    7228 
    7229 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7230 
    7231 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    7232 
    7233 opened ChimeraX session 
    7234 
    7235 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    7236 
    7237 > fly p2 p1 100
    7238 
    7239 > wait
    7240 
    7241 > volume #2-5 show style surface transparency 0.5
    7242 
    7243 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    7244 > bgColor black margin 5
    7245 
    7246 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    7247 > bgColor black margin 5
    7248 
    7249 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    7250 > true bgColor black margin 5
    7251 
    7252 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    7253 > true bgColor black margin 5
    7254 
    7255 > volume all planes z,1743,30
    7256 
    7257 > wait 1700
    7258 
    7259 > volume #1 hide
    7260 
    7261 > wait 1
    7262 
    7263 > volume #2-5 region all
    7264 
    7265 > wait 1
    7266 
    7267 > volume #3-5 transparency 0
    7268 
    7269 > volume #2 transparency 0.6
    7270 
    7271 > zoom 0.85
    7272 
    7273 > wait 5
    7274 
    7275 > roll y 1 360
    7276 
    7277 > wait
    7278 
    7279 executed F107-A3_session.cxc 
    7280 
    7281 > close session
    7282 
    7283 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    7284 
    7285 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7286 step 1, values int8 
    7287 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7288 shown at step 1, values int8 
    7289 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7290 shown at step 1, values int8 
    7291 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7292 shown at step 1, values int8 
    7293 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7294 shown at step 1, values int8 
    7295 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    7296 © 2016-2022 Regents of the University of California. All rights reserved. 
    7297 How to cite UCSF ChimeraX 
    7298 
    7299 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7300 
    7301 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7302 step 2, values int8 
    7303 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7304 shown at level 0.8, step 2, values int8 
    7305 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7306 shown at level 0.8, step 3, values int8 
    7307 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7308 shown at level 0.8, step 2, values int8 
    7309 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7310 shown at level 0.8, step 2, values int8 
    7311 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    7312 the model panel to edit those fields 
    7313 UCSF ChimeraX version: 1.4 (2022-06-03) 
    7314 © 2016-2022 Regents of the University of California. All rights reserved. 
    7315 How to cite UCSF ChimeraX 
    7316 
    7317 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    7318 
    7319 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7320 step 1, values int8 
    7321 
    7322 > volume showOutlineBox true
    7323 
    7324 > volume region all imageMode "full region"
    7325 
    7326 > volume unzone
    7327 
    7328 > mousemode rightMode "crop volume"
    7329 
    7330 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    7331 > "box faces"
    7332 
    7333 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7334 
    7335 > volume #1 region 0,0,0,1385,1409,1604
    7336 
    7337 > volume #1 region all
    7338 
    7339 > volume #1 region 0,0,0,2129,1523,1748
    7340 
    7341 > view orient
    7342 
    7343 > zoom 0.85
    7344 
    7345 > view name p1
    7346 
    7347 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7348 
    7349 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7350 shown at step 1, values int8 
    7351 
    7352 > close #2
    7353 
    7354 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    7355 
    7356 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7357 shown at step 1, values int8 
    7358 
    7359 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    7360 
    7361 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7362 shown at step 1, values int8 
    7363 
    7364 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7365 
    7366 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7367 shown at step 1, values int8 
    7368 
    7369 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    7370 
    7371 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7372 shown at step 1, values int8 
    7373 
    7374 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7375 
    7376 > volume #2 show style surface level 0.8 color #5555ff
    7377 
    7378 > volume #1 region 0,0,0,2129,1523,1740
    7379 
    7380 > volume all region 0,0,0,2129,1523,1740
    7381 
    7382 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7383 > showOutlineBox true imageMode "box faces"
    7384 
    7385 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7386 > showOutlineBox true imageMode "box faces"
    7387 
    7388 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7389 > showOutlineBox true imageMode "box faces"
    7390 
    7391 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    7392 > faces"
    7393 
    7394 > volume #2 show style surface level -50 color #5555ff
    7395 
    7396 > volume #2 show style surface level 10 color #5555ff
    7397 
    7398 > lighting soft
    7399 
    7400 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7401 
    7402 > volume #2 show style surface level 0.8 color #5555ff
    7403 
    7404 > volume #3 show style surface level 0.8 color #aa557f
    7405 
    7406 > volume #4 show style surface level 0.8 color #f514fd
    7407 
    7408 > volume #5 show style surface level 0.8 color #11ffcc
    7409 
    7410 > ~display #1
    7411 
    7412 > volume #2 transparency 0.6
    7413 
    7414 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7415 
    7416 > display #1
    7417 
    7418 > volume all region 0,0,0,2129,1523,1744
    7419 
    7420 > ~display #1
    7421 
    7422 > volume #2 show style surface step 2
    7423 
    7424 > volume #3 show style surface step 3
    7425 
    7426 > volume #4 show style surface step 2
    7427 
    7428 > volume #5 show style surface step 2
    7429 
    7430 > volume #5 show style surface step 1
    7431 
    7432 > volume #5 show style surface step 2
    7433 
    7434 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7435 
    7436 > view name p2
    7437 
    7438 > view list
    7439 
    7440 Named views: p1, p2 
    7441 
    7442 > view p1
    7443 
    7444 > view p2
    7445 
    7446 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7447 
    7448 > fly p2 p1 100
    7449 
    7450 > wait
    7451 
    7452 > view p2
    7453 
    7454 > display #1
    7455 
    7456 > volume #1 region 0,0,0,2129,1523,1744
    7457 
    7458 > volume #1 region 0,0,0,2129,1523,1740
    7459 
    7460 > volume #1 region 0,0,0,2129,1523,1742
    7461 
    7462 > volume #1 region 0,0,0,2129,1523,1743
    7463 
    7464 > volume #1 region 0,0,0,2129,1523,1744
    7465 
    7466 > volume #1 region 0,0,0,2129,1523,1743
    7467 
    7468 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7469 
    7470 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    7471 
    7472 opened ChimeraX session 
    7473 
    7474 > display #1
    7475 
    7476 > ~display #2-5
    7477 
    7478 > display #2-5
    7479 
    7480 > ~display #1
    7481 
    7482 > display #1
    7483 
    7484 > ~display #2-5
    7485 
    7486 > volume all region 0,0,0,2129,1523,1743
    7487 
    7488 > display #2-5
    7489 
    7490 > view p2
    7491 
    7492 > lighting soft
    7493 
    7494 > view p1
    7495 
    7496 > help hide
    7497 
    7498 > hide #1
    7499 
    7500 > view p2
    7501 
    7502 > show #2
    7503 
    7504 > volume #2-5 show style surface
    7505 
    7506 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7507 
    7508 > display #1
    7509 
    7510 > ~display #2-5
    7511 
    7512 > volume #2-5 show style surface
    7513 
    7514 > ~display #2-5
    7515 
    7516 > fly p2 p1 100
    7517 
    7518 > wait
    7519 
    7520 > volume #2-5 show style surface transparency 0.5
    7521 
    7522 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    7523 > bgColor black margin 5
    7524 
    7525 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    7526 > bgColor black margin 5
    7527 
    7528 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    7529 > true bgColor black margin 5
    7530 
    7531 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    7532 > true bgColor black margin 5
    7533 
    7534 > volume all planes z,1743,30
    7535 
    7536 > wait 1700
    7537 
    7538 > close session
    7539 
    7540 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    7541 
    7542 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7543 step 1, values int8 
    7544 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7545 shown at level 0.8, step 1, values int8 
    7546 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7547 shown at level 0.8, step 1, values int8 
    7548 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7549 shown at level 0.8, step 1, values int8 
    7550 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7551 shown at level 0.8, step 1, values int8 
    7552 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    7553 © 2016-2022 Regents of the University of California. All rights reserved. 
    7554 How to cite UCSF ChimeraX 
    7555 
    7556 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7557 
    7558 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7559 step 2, values int8 
    7560 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7561 shown at level 0.8, step 2, values int8 
    7562 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7563 shown at level 0.8, step 3, values int8 
    7564 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7565 shown at level 0.8, step 2, values int8 
    7566 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7567 shown at level 0.8, step 2, values int8 
    7568 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    7569 the model panel to edit those fields 
    7570 UCSF ChimeraX version: 1.4 (2022-06-03) 
    7571 © 2016-2022 Regents of the University of California. All rights reserved. 
    7572 How to cite UCSF ChimeraX 
    7573 
    7574 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    7575 
    7576 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7577 step 1, values int8 
    7578 
    7579 > volume showOutlineBox true
    7580 
    7581 > volume region all imageMode "full region"
    7582 
    7583 > volume unzone
    7584 
    7585 > mousemode rightMode "crop volume"
    7586 
    7587 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    7588 > "box faces"
    7589 
    7590 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7591 
    7592 > volume #1 region 0,0,0,1385,1409,1604
    7593 
    7594 > volume #1 region all
    7595 
    7596 > volume #1 region 0,0,0,2129,1523,1748
    7597 
    7598 > view orient
    7599 
    7600 > zoom 0.85
    7601 
    7602 > view name p1
    7603 
    7604 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7605 
    7606 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7607 shown at step 1, values int8 
    7608 
    7609 > close #2
    7610 
    7611 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    7612 
    7613 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7614 shown at step 1, values int8 
    7615 
    7616 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    7617 
    7618 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7619 shown at step 1, values int8 
    7620 
    7621 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7622 
    7623 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7624 shown at step 1, values int8 
    7625 
    7626 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    7627 
    7628 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7629 shown at step 1, values int8 
    7630 
    7631 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7632 
    7633 > volume #2 show style surface level 0.8 color #5555ff
    7634 
    7635 > volume #1 region 0,0,0,2129,1523,1740
    7636 
    7637 > volume all region 0,0,0,2129,1523,1740
    7638 
    7639 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7640 > showOutlineBox true imageMode "box faces"
    7641 
    7642 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7643 > showOutlineBox true imageMode "box faces"
    7644 
    7645 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7646 > showOutlineBox true imageMode "box faces"
    7647 
    7648 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    7649 > faces"
    7650 
    7651 > volume #2 show style surface level -50 color #5555ff
    7652 
    7653 > volume #2 show style surface level 10 color #5555ff
    7654 
    7655 > lighting soft
    7656 
    7657 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7658 
    7659 > volume #2 show style surface level 0.8 color #5555ff
    7660 
    7661 > volume #3 show style surface level 0.8 color #aa557f
    7662 
    7663 > volume #4 show style surface level 0.8 color #f514fd
    7664 
    7665 > volume #5 show style surface level 0.8 color #11ffcc
    7666 
    7667 > ~display #1
    7668 
    7669 > volume #2 transparency 0.6
    7670 
    7671 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7672 
    7673 > display #1
    7674 
    7675 > volume all region 0,0,0,2129,1523,1744
    7676 
    7677 > ~display #1
    7678 
    7679 > volume #2 show style surface step 2
    7680 
    7681 > volume #3 show style surface step 3
    7682 
    7683 > volume #4 show style surface step 2
    7684 
    7685 > volume #5 show style surface step 2
    7686 
    7687 > volume #5 show style surface step 1
    7688 
    7689 > volume #5 show style surface step 2
    7690 
    7691 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7692 
    7693 > view name p2
    7694 
    7695 > view list
    7696 
    7697 Named views: p1, p2 
    7698 
    7699 > view p1
    7700 
    7701 > view p2
    7702 
    7703 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7704 
    7705 > fly p2 p1 100
    7706 
    7707 > wait
    7708 
    7709 > view p2
    7710 
    7711 > display #1
    7712 
    7713 > volume #1 region 0,0,0,2129,1523,1744
    7714 
    7715 > volume #1 region 0,0,0,2129,1523,1740
    7716 
    7717 > volume #1 region 0,0,0,2129,1523,1742
    7718 
    7719 > volume #1 region 0,0,0,2129,1523,1743
    7720 
    7721 > volume #1 region 0,0,0,2129,1523,1744
    7722 
    7723 > volume #1 region 0,0,0,2129,1523,1743
    7724 
    7725 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7726 
    7727 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    7728 
    7729 opened ChimeraX session 
    7730 
    7731 > display #1
    7732 
    7733 > ~display #2-5
    7734 
    7735 > display #2-5
    7736 
    7737 > ~display #1
    7738 
    7739 > display #1
    7740 
    7741 > ~display #2-5
    7742 
    7743 > volume all region 0,0,0,2129,1523,1743
    7744 
    7745 > display #2-5
    7746 
    7747 > view p2
    7748 
    7749 > lighting soft
    7750 
    7751 > view p1
    7752 
    7753 > help hide
    7754 
    7755 > hide #1
    7756 
    7757 > view p2
    7758 
    7759 > show #2
    7760 
    7761 > volume #2-5 show style surface
    7762 
    7763 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7764 
    7765 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    7766 
    7767 opened ChimeraX session 
    7768 
    7769 > display #1
    7770 
    7771 > ~display #2-5
    7772 
    7773 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7774 
    7775 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    7776 
    7777 opened ChimeraX session 
    7778 
    7779 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    7780 
    7781 > fly p2 p1 100
    7782 
    7783 > wait
    7784 
    7785 > volume #2-5 show style surface transparency 0.5
    7786 
    7787 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    7788 > bgColor black margin 5
    7789 
    7790 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    7791 > bgColor black margin 5
    7792 
    7793 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    7794 > true bgColor black margin 5
    7795 
    7796 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    7797 > true bgColor black margin 5
    7798 
    7799 > volume all planes z,1743,30
    7800 
    7801 > wait 1743
    7802 
    7803 > volume #1 hide
    7804 
    7805 > wait 1
    7806 
    7807 > volume #2-5 region all
    7808 
    7809 > wait 1
    7810 
    7811 > volume #3-5 transparency 0
    7812 
    7813 > volume #2 transparency 0.6
    7814 
    7815 executed F107-A3_session.cxc 
    7816 
    7817 > zoom 0.85
    7818 
    7819 > wait 5
    7820 
    7821 > oll y 1 360; wait;
    7822 
    7823 Unknown command: oll y 1 360; wait; 
    7824 
    7825 > roll y 1 360
    7826 
    7827 > wait
    7828 
    7829 > fly p1 p2 100
    7830 
    7831 > wait
    7832 
    7833 > view p1
    7834 
    7835 > roll y 1 360
    7836 
    7837 > wait
    7838 
    7839 > fly p1 p2 100
    7840 
    7841 > wait
    7842 
    7843 > close session
    7844 
    7845 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    7846 
    7847 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7848 step 1, values int8 
    7849 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7850 shown at step 1, values int8 
    7851 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7852 shown at step 1, values int8 
    7853 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7854 shown at step 1, values int8 
    7855 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7856 shown at step 1, values int8 
    7857 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    7858 © 2016-2022 Regents of the University of California. All rights reserved. 
    7859 How to cite UCSF ChimeraX 
    7860 
    7861 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7862 
    7863 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7864 step 2, values int8 
    7865 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7866 shown at level 0.8, step 2, values int8 
    7867 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7868 shown at level 0.8, step 3, values int8 
    7869 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7870 shown at level 0.8, step 2, values int8 
    7871 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7872 shown at level 0.8, step 2, values int8 
    7873 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    7874 the model panel to edit those fields 
    7875 UCSF ChimeraX version: 1.4 (2022-06-03) 
    7876 © 2016-2022 Regents of the University of California. All rights reserved. 
    7877 How to cite UCSF ChimeraX 
    7878 
    7879 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    7880 
    7881 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    7882 step 1, values int8 
    7883 
    7884 > volume showOutlineBox true
    7885 
    7886 > volume region all imageMode "full region"
    7887 
    7888 > volume unzone
    7889 
    7890 > mousemode rightMode "crop volume"
    7891 
    7892 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    7893 > "box faces"
    7894 
    7895 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7896 
    7897 > volume #1 region 0,0,0,1385,1409,1604
    7898 
    7899 > volume #1 region all
    7900 
    7901 > volume #1 region 0,0,0,2129,1523,1748
    7902 
    7903 > view orient
    7904 
    7905 > zoom 0.85
    7906 
    7907 > view name p1
    7908 
    7909 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7910 
    7911 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7912 shown at step 1, values int8 
    7913 
    7914 > close #2
    7915 
    7916 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    7917 
    7918 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    7919 shown at step 1, values int8 
    7920 
    7921 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    7922 
    7923 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    7924 shown at step 1, values int8 
    7925 
    7926 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    7927 
    7928 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    7929 shown at step 1, values int8 
    7930 
    7931 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    7932 
    7933 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    7934 shown at step 1, values int8 
    7935 
    7936 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7937 
    7938 > volume #2 show style surface level 0.8 color #5555ff
    7939 
    7940 > volume #1 region 0,0,0,2129,1523,1740
    7941 
    7942 > volume all region 0,0,0,2129,1523,1740
    7943 
    7944 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7945 > showOutlineBox true imageMode "box faces"
    7946 
    7947 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7948 > showOutlineBox true imageMode "box faces"
    7949 
    7950 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    7951 > showOutlineBox true imageMode "box faces"
    7952 
    7953 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    7954 > faces"
    7955 
    7956 > volume #2 show style surface level -50 color #5555ff
    7957 
    7958 > volume #2 show style surface level 10 color #5555ff
    7959 
    7960 > lighting soft
    7961 
    7962 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7963 
    7964 > volume #2 show style surface level 0.8 color #5555ff
    7965 
    7966 > volume #3 show style surface level 0.8 color #aa557f
    7967 
    7968 > volume #4 show style surface level 0.8 color #f514fd
    7969 
    7970 > volume #5 show style surface level 0.8 color #11ffcc
    7971 
    7972 > ~display #1
    7973 
    7974 > volume #2 transparency 0.6
    7975 
    7976 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7977 
    7978 > display #1
    7979 
    7980 > volume all region 0,0,0,2129,1523,1744
    7981 
    7982 > ~display #1
    7983 
    7984 > volume #2 show style surface step 2
    7985 
    7986 > volume #3 show style surface step 3
    7987 
    7988 > volume #4 show style surface step 2
    7989 
    7990 > volume #5 show style surface step 2
    7991 
    7992 > volume #5 show style surface step 1
    7993 
    7994 > volume #5 show style surface step 2
    7995 
    7996 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    7997 
    7998 > view name p2
    7999 
    8000 > view list
    8001 
    8002 Named views: p1, p2 
    8003 
    8004 > view p1
    8005 
    8006 > view p2
    8007 
    8008 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8009 
    8010 > fly p2 p1 100
    8011 
    8012 > wait
    8013 
    8014 > view p2
    8015 
    8016 > display #1
    8017 
    8018 > volume #1 region 0,0,0,2129,1523,1744
    8019 
    8020 > volume #1 region 0,0,0,2129,1523,1740
    8021 
    8022 > volume #1 region 0,0,0,2129,1523,1742
    8023 
    8024 > volume #1 region 0,0,0,2129,1523,1743
    8025 
    8026 > volume #1 region 0,0,0,2129,1523,1744
    8027 
    8028 > volume #1 region 0,0,0,2129,1523,1743
    8029 
    8030 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8031 
    8032 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    8033 
    8034 opened ChimeraX session 
    8035 
    8036 > display #1
    8037 
    8038 > ~display #2-5
    8039 
    8040 > display #2-5
    8041 
    8042 > ~display #1
    8043 
    8044 > display #1
    8045 
    8046 > ~display #2-5
    8047 
    8048 > volume all region 0,0,0,2129,1523,1743
    8049 
    8050 > display #2-5
    8051 
    8052 > view p2
    8053 
    8054 > lighting soft
    8055 
    8056 > view p1
    8057 
    8058 > help hide
    8059 
    8060 > hide #1
    8061 
    8062 > view p2
    8063 
    8064 > show #2
    8065 
    8066 > volume #2-5 show style surface
    8067 
    8068 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8069 
    8070 > display #1
    8071 
    8072 > ~display #2-5
    8073 
    8074 > volume #2-5 show style surface
    8075 
    8076 > ~display #2-5
    8077 
    8078 > fly p2 p1 100
    8079 
    8080 > wait
    8081 
    8082 > volume #2-5 show style surface transparency 0.5
    8083 
    8084 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    8085 > bgColor black margin 5
    8086 
    8087 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    8088 > bgColor black margin 5
    8089 
    8090 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    8091 > true bgColor black margin 5
    8092 
    8093 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    8094 > true bgColor black margin 5
    8095 
    8096 > volume all planes z,1743,30
    8097 
    8098 > wait 1700
    8099 
    8100 > close session
    8101 
    8102 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    8103 
    8104 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8105 step 1, values int8 
    8106 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8107 shown at level 0.8, step 1, values int8 
    8108 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8109 shown at level 0.8, step 1, values int8 
    8110 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8111 shown at level 0.8, step 1, values int8 
    8112 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8113 shown at level 0.8, step 1, values int8 
    8114 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    8115 © 2016-2022 Regents of the University of California. All rights reserved. 
    8116 How to cite UCSF ChimeraX 
    8117 
    8118 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8119 
    8120 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8121 step 2, values int8 
    8122 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8123 shown at level 0.8, step 2, values int8 
    8124 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8125 shown at level 0.8, step 3, values int8 
    8126 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8127 shown at level 0.8, step 2, values int8 
    8128 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8129 shown at level 0.8, step 2, values int8 
    8130 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    8131 the model panel to edit those fields 
    8132 UCSF ChimeraX version: 1.4 (2022-06-03) 
    8133 © 2016-2022 Regents of the University of California. All rights reserved. 
    8134 How to cite UCSF ChimeraX 
    8135 
    8136 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    8137 
    8138 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8139 step 1, values int8 
    8140 
    8141 > volume showOutlineBox true
    8142 
    8143 > volume region all imageMode "full region"
    8144 
    8145 > volume unzone
    8146 
    8147 > mousemode rightMode "crop volume"
    8148 
    8149 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    8150 > "box faces"
    8151 
    8152 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8153 
    8154 > volume #1 region 0,0,0,1385,1409,1604
    8155 
    8156 > volume #1 region all
    8157 
    8158 > volume #1 region 0,0,0,2129,1523,1748
    8159 
    8160 > view orient
    8161 
    8162 > zoom 0.85
    8163 
    8164 > view name p1
    8165 
    8166 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8167 
    8168 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8169 shown at step 1, values int8 
    8170 
    8171 > close #2
    8172 
    8173 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    8174 
    8175 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8176 shown at step 1, values int8 
    8177 
    8178 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    8179 
    8180 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8181 shown at step 1, values int8 
    8182 
    8183 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8184 
    8185 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8186 shown at step 1, values int8 
    8187 
    8188 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    8189 
    8190 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8191 shown at step 1, values int8 
    8192 
    8193 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8194 
    8195 > volume #2 show style surface level 0.8 color #5555ff
    8196 
    8197 > volume #1 region 0,0,0,2129,1523,1740
    8198 
    8199 > volume all region 0,0,0,2129,1523,1740
    8200 
    8201 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8202 > showOutlineBox true imageMode "box faces"
    8203 
    8204 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8205 > showOutlineBox true imageMode "box faces"
    8206 
    8207 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8208 > showOutlineBox true imageMode "box faces"
    8209 
    8210 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    8211 > faces"
    8212 
    8213 > volume #2 show style surface level -50 color #5555ff
    8214 
    8215 > volume #2 show style surface level 10 color #5555ff
    8216 
    8217 > lighting soft
    8218 
    8219 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8220 
    8221 > volume #2 show style surface level 0.8 color #5555ff
    8222 
    8223 > volume #3 show style surface level 0.8 color #aa557f
    8224 
    8225 > volume #4 show style surface level 0.8 color #f514fd
    8226 
    8227 > volume #5 show style surface level 0.8 color #11ffcc
    8228 
    8229 > ~display #1
    8230 
    8231 > volume #2 transparency 0.6
    8232 
    8233 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8234 
    8235 > display #1
    8236 
    8237 > volume all region 0,0,0,2129,1523,1744
    8238 
    8239 > ~display #1
    8240 
    8241 > volume #2 show style surface step 2
    8242 
    8243 > volume #3 show style surface step 3
    8244 
    8245 > volume #4 show style surface step 2
    8246 
    8247 > volume #5 show style surface step 2
    8248 
    8249 > volume #5 show style surface step 1
    8250 
    8251 > volume #5 show style surface step 2
    8252 
    8253 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8254 
    8255 > view name p2
    8256 
    8257 > view list
    8258 
    8259 Named views: p1, p2 
    8260 
    8261 > view p1
    8262 
    8263 > view p2
    8264 
    8265 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8266 
    8267 > fly p2 p1 100
    8268 
    8269 > wait
    8270 
    8271 > view p2
    8272 
    8273 > display #1
    8274 
    8275 > volume #1 region 0,0,0,2129,1523,1744
    8276 
    8277 > volume #1 region 0,0,0,2129,1523,1740
    8278 
    8279 > volume #1 region 0,0,0,2129,1523,1742
    8280 
    8281 > volume #1 region 0,0,0,2129,1523,1743
    8282 
    8283 > volume #1 region 0,0,0,2129,1523,1744
    8284 
    8285 > volume #1 region 0,0,0,2129,1523,1743
    8286 
    8287 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8288 
    8289 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    8290 
    8291 opened ChimeraX session 
    8292 
    8293 > display #1
    8294 
    8295 > ~display #2-5
    8296 
    8297 > display #2-5
    8298 
    8299 > ~display #1
    8300 
    8301 > display #1
    8302 
    8303 > ~display #2-5
    8304 
    8305 > volume all region 0,0,0,2129,1523,1743
    8306 
    8307 > display #2-5
    8308 
    8309 > view p2
    8310 
    8311 > lighting soft
    8312 
    8313 > view p1
    8314 
    8315 > help hide
    8316 
    8317 > hide #1
    8318 
    8319 > view p2
    8320 
    8321 > show #2
    8322 
    8323 > volume #2-5 show style surface
    8324 
    8325 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8326 
    8327 ——— End of log from Wed Jul 27 14:08:40 2022 ———
    8328 
    8329 opened ChimeraX session 
    8330 
    8331 > display #1
    8332 
    8333 > ~display #2-5
    8334 
    8335 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8336 
    8337 ——— End of log from Wed Jul 27 14:27:32 2022 ———
    8338 
    8339 opened ChimeraX session 
    8340 
    8341 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
    8342 
    8343 > fly p2 p1 100
    8344 
    8345 > wait
    8346 
    8347 > volume #2-5 show style surface transparency 0.5
    8348 
    8349 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    8350 > bgColor black margin 5
    8351 
    8352 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    8353 > bgColor black margin 5
    8354 
    8355 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    8356 > true bgColor black margin 5
    8357 
    8358 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    8359 > true bgColor black margin 5
    8360 
    8361 > volume all planes z,1743,30
    8362 
    8363 > wait 1743
    8364 
    8365 > volume #1 hide
    8366 
    8367 > wait 1
    8368 
    8369 > volume #2-5 region all
    8370 
    8371 > wait 1
    8372 
    8373 > volume #3-5 transparency 0
    8374 
    8375 > volume #2 transparency 0.6
    8376 
    8377 > roll y 1 360
    8378 
    8379 > wait
    8380 
    8381 > fly p1 p2 100
    8382 
    8383 > wait
    8384 
    8385 executed F107-A3_session.cxc 
    8386 
    8387 > close session
    8388 
    8389 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    8390 
    8391 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8392 step 1, values int8 
    8393 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8394 shown at step 1, values int8 
    8395 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8396 shown at step 1, values int8 
    8397 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8398 shown at step 1, values int8 
    8399 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8400 shown at step 1, values int8 
    8401 Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    8402 © 2016-2022 Regents of the University of California. All rights reserved. 
    8403 How to cite UCSF ChimeraX 
    8404 
    8405 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8406 
    8407 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8408 step 2, values int8 
    8409 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8410 shown at level 0.8, step 2, values int8 
    8411 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8412 shown at level 0.8, step 3, values int8 
    8413 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8414 shown at level 0.8, step 2, values int8 
    8415 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8416 shown at level 0.8, step 2, values int8 
    8417 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    8418 the model panel to edit those fields 
    8419 UCSF ChimeraX version: 1.4 (2022-06-03) 
    8420 © 2016-2022 Regents of the University of California. All rights reserved. 
    8421 How to cite UCSF ChimeraX 
    8422 
    8423 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    8424 
    8425 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8426 step 1, values int8 
    8427 
    8428 > volume showOutlineBox true
    8429 
    8430 > volume region all imageMode "full region"
    8431 
    8432 > volume unzone
    8433 
    8434 > mousemode rightMode "crop volume"
    8435 
    8436 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    8437 > "box faces"
    8438 
    8439 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8440 
    8441 > volume #1 region 0,0,0,1385,1409,1604
    8442 
    8443 > volume #1 region all
    8444 
    8445 > volume #1 region 0,0,0,2129,1523,1748
    8446 
    8447 > view orient
    8448 
    8449 > zoom 0.85
    8450 
    8451 > view name p1
    8452 
    8453 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8454 
    8455 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8456 shown at step 1, values int8 
    8457 
    8458 > close #2
    8459 
    8460 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    8461 
    8462 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8463 shown at step 1, values int8 
    8464 
    8465 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    8466 
    8467 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8468 shown at step 1, values int8 
    8469 
    8470 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8471 
    8472 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8473 shown at step 1, values int8 
    8474 
    8475 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    8476 
    8477 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8478 shown at step 1, values int8 
    8479 
    8480 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8481 
    8482 > volume #2 show style surface level 0.8 color #5555ff
    8483 
    8484 > volume #1 region 0,0,0,2129,1523,1740
    8485 
    8486 > volume all region 0,0,0,2129,1523,1740
    8487 
    8488 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8489 > showOutlineBox true imageMode "box faces"
    8490 
    8491 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8492 > showOutlineBox true imageMode "box faces"
    8493 
    8494 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8495 > showOutlineBox true imageMode "box faces"
    8496 
    8497 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    8498 > faces"
    8499 
    8500 > volume #2 show style surface level -50 color #5555ff
    8501 
    8502 > volume #2 show style surface level 10 color #5555ff
    8503 
    8504 > lighting soft
    8505 
    8506 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8507 
    8508 > volume #2 show style surface level 0.8 color #5555ff
    8509 
    8510 > volume #3 show style surface level 0.8 color #aa557f
    8511 
    8512 > volume #4 show style surface level 0.8 color #f514fd
    8513 
    8514 > volume #5 show style surface level 0.8 color #11ffcc
    8515 
    8516 > ~display #1
    8517 
    8518 > volume #2 transparency 0.6
    8519 
    8520 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8521 
    8522 > display #1
    8523 
    8524 > volume all region 0,0,0,2129,1523,1744
    8525 
    8526 > ~display #1
    8527 
    8528 > volume #2 show style surface step 2
    8529 
    8530 > volume #3 show style surface step 3
    8531 
    8532 > volume #4 show style surface step 2
    8533 
    8534 > volume #5 show style surface step 2
    8535 
    8536 > volume #5 show style surface step 1
    8537 
    8538 > volume #5 show style surface step 2
    8539 
    8540 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8541 
    8542 > view name p2
    8543 
    8544 > view list
    8545 
    8546 Named views: p1, p2 
    8547 
    8548 > view p1
    8549 
    8550 > view p2
    8551 
    8552 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8553 
    8554 > fly p2 p1 100
    8555 
    8556 > wait
    8557 
    8558 > view p2
    8559 
    8560 > display #1
    8561 
    8562 > volume #1 region 0,0,0,2129,1523,1744
    8563 
    8564 > volume #1 region 0,0,0,2129,1523,1740
    8565 
    8566 > volume #1 region 0,0,0,2129,1523,1742
    8567 
    8568 > volume #1 region 0,0,0,2129,1523,1743
    8569 
    8570 > volume #1 region 0,0,0,2129,1523,1744
    8571 
    8572 > volume #1 region 0,0,0,2129,1523,1743
    8573 
    8574 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8575 
    8576 ——— End of log from Wed Jul 27 13:49:38 2022 ———
    8577 
    8578 opened ChimeraX session 
    8579 
    8580 > display #1
    8581 
    8582 > ~display #2-5
    8583 
    8584 > display #2-5
    8585 
    8586 > ~display #1
    8587 
    8588 > display #1
    8589 
    8590 > ~display #2-5
    8591 
    8592 > volume all region 0,0,0,2129,1523,1743
    8593 
    8594 > display #2-5
    8595 
    8596 > view p2
    8597 
    8598 > lighting soft
    8599 
    8600 > view p1
    8601 
    8602 > help hide
    8603 
    8604 > hide #1
    8605 
    8606 > view p2
    8607 
    8608 > show #2
    8609 
    8610 > volume #2-5 show style surface
    8611 
    8612 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8613 
    8614 > display #1
    8615 
    8616 > ~display #2-5
    8617 
    8618 > volume #2-5 show style surface
    8619 
    8620 > ~display #2-5
    8621 
    8622 > fly p2 p1 100
    8623 
    8624 > wait
    8625 
    8626 > volume #2-5 show style surface transparency 0.5
    8627 
    8628 > 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
    8629 > bgColor black margin 5
    8630 
    8631 > 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
    8632 > bgColor black margin 5
    8633 
    8634 > 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
    8635 > true bgColor black margin 5
    8636 
    8637 > 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
    8638 > true bgColor black margin 5
    8639 
    8640 > volume all planes z,1743,30
    8641 
    8642 > wait 1700
    8643 
    8644 > close session
    8645 
    8646 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
    8647 
    8648 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8649 step 1, values int8 
    8650 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8651 shown at level 0.8, step 1, values int8 
    8652 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8653 shown at level 0.8, step 1, values int8 
    8654 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8655 shown at level 0.8, step 1, values int8 
    8656 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8657 shown at level 0.8, step 1, values int8 
    8658 Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    8659 © 2016-2022 Regents of the University of California. All rights reserved. 
    8660 How to cite UCSF ChimeraX 
    8661 
    8662 > open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8663 
    8664 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8665 step 2, values int8 
    8666 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8667 shown at level 0.8, step 2, values int8 
    8668 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8669 shown at level 0.8, step 3, values int8 
    8670 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8671 shown at level 0.8, step 2, values int8 
    8672 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8673 shown at level 0.8, step 2, values int8 
    8674 Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
    8675 the model panel to edit those fields 
    8676 UCSF ChimeraX version: 1.4 (2022-06-03) 
    8677 © 2016-2022 Regents of the University of California. All rights reserved. 
    8678 How to cite UCSF ChimeraX 
    8679 
    8680 > open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
    8681 
    8682 Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
    8683 step 1, values int8 
    8684 
    8685 > volume showOutlineBox true
    8686 
    8687 > volume region all imageMode "full region"
    8688 
    8689 > volume unzone
    8690 
    8691 > mousemode rightMode "crop volume"
    8692 
    8693 > volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
    8694 > "box faces"
    8695 
    8696 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8697 
    8698 > volume #1 region 0,0,0,1385,1409,1604
    8699 
    8700 > volume #1 region all
    8701 
    8702 > volume #1 region 0,0,0,2129,1523,1748
    8703 
    8704 > view orient
    8705 
    8706 > zoom 0.85
    8707 
    8708 > view name p1
    8709 
    8710 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8711 
    8712 Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8713 shown at step 1, values int8 
    8714 
    8715 > close #2
    8716 
    8717 > open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
    8718 
    8719 Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
    8720 shown at step 1, values int8 
    8721 
    8722 > open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
    8723 
    8724 Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
    8725 shown at step 1, values int8 
    8726 
    8727 > open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
    8728 
    8729 Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
    8730 shown at step 1, values int8 
    8731 
    8732 > open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
    8733 
    8734 Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
    8735 shown at step 1, values int8 
    8736 
    8737 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8738 
    8739 > volume #2 show style surface level 0.8 color #5555ff
    8740 
    8741 > volume #1 region 0,0,0,2129,1523,1740
    8742 
    8743 > volume all region 0,0,0,2129,1523,1740
    8744 
    8745 > volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8746 > showOutlineBox true imageMode "box faces"
    8747 
    8748 > volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8749 > showOutlineBox true imageMode "box faces"
    8750 
    8751 > volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
    8752 > showOutlineBox true imageMode "box faces"
    8753 
    8754 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
    8755 > faces"
    8756 
    8757 > volume #2 show style surface level -50 color #5555ff
    8758 
    8759 > volume #2 show style surface level 10 color #5555ff
    8760 
    8761 > lighting soft
    8762 
    8763 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8764 
    8765 > volume #2 show style surface level 0.8 color #5555ff
    8766 
    8767 > volume #3 show style surface level 0.8 color #aa557f
    8768 
    8769 > volume #4 show style surface level 0.8 color #f514fd
    8770 
    8771 > volume #5 show style surface level 0.8 color #11ffcc
    8772 
    8773 > ~display #1
    8774 
    8775 > volume #2 transparency 0.6
    8776 
    8777 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8778 
    8779 > display #1
    8780 
    8781 > volume all region 0,0,0,2129,1523,1744
    8782 
    8783 > ~display #1
    8784 
    8785 > volume #2 show style surface step 2
    8786 
    8787 > volume #3 show style surface step 3
    8788 
    8789 > volume #4 show style surface step 2
    8790 
    8791 > volume #5 show style surface step 2
    8792 
    8793 > volume #5 show style surface step 1
    8794 
    8795 > volume #5 show style surface step 2
    8796 
    8797 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8798 
    8799 > view name p2
    8800 
    8801 > view list
    8802 
    8803 Named views: p1, p2 
    8804 
    8805 > view p1
    8806 
    8807 > view p2
    8808 
    8809 > save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
    8810 
    8811 > fly p2 p1 100
    8812 
    8813 > wait
    8814 
    8815 > view p2
    8816 
    8817 > display #1
    8818 
    8819 > volume #1 region 0,0,0,2129,1523,1744
    8820 
    8821 > volume #1 region 0,0,0,2129,1523,1740
    8822 
    8823 > volume #1 region 0,0,0,2129,1523,1742
    8824 
    8825 > volume #1 region 0,0,0,2129,1523,1743
     1988
     1989[deleted much of the log to fit within ticket length limits]
    88261990
    88271991> volume #1 region 0,0,0,2129,1523,1744