The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Error from UniProt web server while checking job status: HTTP Error 400:
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\fern0096\Desktop\CHEM5760\Binding site.cxs" format session
Log from Thu Oct 23 03:11:07 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7NVH
7nvh title:
Cryo-EM structure of the mycolic acid transporter MmpL3 from M. tuberculosis
[more info...]
Chain information for 7nvh #1
---
Chain | Description | UniProt
A | Trehalose monomycolate exporter MmpL3 | MMPL3_MYCTU 1-753
Non-standard residues in 7nvh #1
---
AV0 — Lauryl Maltose Neopentyl Glycol (2,2-didecylpropane-1,3-bis-b-D-
maltopyranoside; 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranoside)
19 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Alignment identifier is 1/A
> select :AV0
69 atoms, 72 bonds, 1 residue, 1 model selected
> color sel white
> color sel orange
> set bgColor white
> color sel byhetero
> select /A:1-752
5440 atoms, 5555 bonds, 1 pseudobond, 717 residues, 2 models selected
> color (#!1 & sel) hot pink
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaff7fff
> color (#!1 & sel) #00557fff
> color (#!1 & sel) #aa00ffff
> color (#!1 & sel) #aa007fff
> color (#!1 & sel) #005500ff
> color (#!1 & sel) #aa5500ff
> color (#!1 & sel) #ff0000ff
> color (#!1 & sel) #ff007fff
> color (#!1 & sel) #ff00ffff
> color (#!1 & sel) #5500ffff
> color (#!1 & sel) #ff557fff
> color (#!1 & sel) #55aa00ff
> color (#!1 & sel) #aaaaffff
> color (#!1 & sel) #a9a9fdff
> color (#!1 & sel) #a0a0f0ff
> color (#!1 & sel) #a3a3f4ff
> color (#!1 & sel) #a1a1f1ff
> color (#!1 & sel) #9999e5ff
> color (#!1 & sel) #8383c5ff
> color (#!1 & sel) #8282c3ff
> color (#!1 & sel) #7575b0ff
> color (#!1 & sel) #7373adff
> color (#!1 & sel) #7272abff
> color (#!1 & sel) #666699ff
> color (#!1 & sel) #656598ff
> color (#!1 & sel) #646496ff
> color (#!1 & sel) #53537dff
> color (#!1 & sel) #53537cff
> color (#!1 & sel) #53537dff
> color (#!1 & sel) #4e4e75ff
> color (#!1 & sel) #2a2a3fff
> color (#!1 & sel) #2b2b41ff
> color (#!1 & sel) #2c2c42ff
> color (#!1 & sel) #2f2f46ff
> color (#!1 & sel) #31314aff
> color (#!1 & sel) #33334dff
> color (#!1 & sel) #414161ff
> color (#!1 & sel) #444466ff
> color (#!1 & sel) #4d4d74ff
> color (#!1 & sel) #53537dff
> color (#!1 & sel) #575782ff
> color (#!1 & sel) #646496ff
> color (#!1 & sel) #656598ff
> color (#!1 & sel) #625e98ff
> color (#!1 & sel) #646098ff
> color (#!1 & sel) #686698ff
> color (#!1 & sel) #6d6c98ff
> color (#!1 & sel) #6f6d98ff
> color (#!1 & sel) #787698ff
> color (#!1 & sel) #7a7898ff
> color (#!1 & sel) #7b7898ff
> color (#!1 & sel) #7a7898ff
> color (#!1 & sel) #787598ff
> color (#!1 & sel) #747298ff
> color (#!1 & sel) #737198ff
> color (#!1 & sel) #727198ff
> color (#!1 & sel) #6d6c98ff
> color (#!1 & sel) #646498ff
> color (#!1 & sel) #5a6098ff
> color (#!1 & sel) #585f98ff
> color (#!1 & sel) #585e98ff
> color (#!1 & sel) #575e98ff
> color (#!1 & sel) #526198ff
> color (#!1 & sel) #4c6098ff
> color (#!1 & sel) #4d6198ff
> color (#!1 & sel) #4d5f98ff
> color (#!1 & sel) #4d5e98ff
> color (#!1 & sel) #4f5a98ff
> color (#!1 & sel) #505b98ff
> color (#!1 & sel) #505a98ff
> color (#!1 & sel) #505898ff
> color (#!1 & sel) #505598ff
> select clear
> select /A:1-752
5440 atoms, 5555 bonds, 1 pseudobond, 717 residues, 2 models selected
> color (#!1 & sel) byhetero
> select clear
> select /A:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel forest green
> color sel #aaff7fff
> color sel #a0ff78ff
> color sel #97ff77ff
> color sel #73ff69ff
> color sel #70ff66ff
> color sel #6dff63ff
> color sel #6bff63ff
> color sel #65ff62ff
> color sel #61ff6cff
> color sel #60ff6dff
> color sel #5eff6bff
> color sel #5aff73ff
> color sel #4bff84ff
> color sel #47ff84ff
> color sel #42ff87ff
> color sel #35ff86ff
> color sel #33ff85ff
> color sel #31ff83ff
> color sel #26ff9aff
> color sel #14ffc4ff
> color sel #13ffd0ff
> color sel #13ffd8ff
> color sel #14ffd8ff
> color sel #14ffdcff
> color sel #15ffdcff
> color sel #17ffdcff
> color sel #18ffdcff
> color sel #19ffdcff
> color sel #1affddff
> color sel #1cffddff
> color sel #1dffddff
> color sel #1effd9ff
> color sel #1effd2ff
> color sel #21ffd3ff
> color sel #23ffc8ff
> color sel #23ffb6ff
> color sel #23ffabff
> color sel #23ff9cff
> color sel #23ff98ff
> color sel #23ff9cff
> color sel #23ffa3ff
> color sel #00aa7fff
> color sel #00a87bff
> color sel #009d73ff
> color sel #009c72ff
> color sel #009970ff
> color sel #00986fff
> color sel #008763ff
> color sel #008461ff
> color sel #00825fff
> color sel #008360ff
> color sel #008662ff
> color sel #008a65ff
> color sel #008c67ff
> color sel #008d67ff
> color sel #00906aff
> color sel #00916aff
> color sel #00ff7fff
> color sel #55ff7fff
> color sel #55aa00ff
> color sel #2faa56ff
> color sel #31aa57ff
> color sel #31aa58ff
> color sel #41aa68ff
> color sel #4eaa73ff
> color sel #55aa77ff
> color sel #5faa7bff
> color sel #68aa82ff
> color sel #69aa83ff
> color sel #69aa84ff
> color sel #6baa85ff
> color sel #6baa88ff
> color sel #6baa89ff
> color sel #6baa8bff
> color sel #69aa8cff
> color sel #68aa8bff
> color sel #67aa8bff
> color sel #66aa8aff
> color sel #65aa8aff
> color sel #63aa89ff
> color sel #63aa8aff
> color sel #62aa8aff
> color sel #62aa8cff
> color sel #61aa8cff
> color sel #3baa7cff
> color sel #22aa6dff
> color sel #16aa65ff
> color sel #11aa63ff
> color sel #10aa62ff
> color sel #10aa65ff
> color sel #11aa7cff
> color sel #1d8baaff
> color sel #2743aaff
> color sel #2831aaff
> color sel #292faaff
> color sel #2b31aaff
> color sel #2f9aaaff
> color sel #3baa6fff
> color sel #52aa5fff
> color sel #65aa75ff
> color sel #6eaa81ff
> color sel #6faa84ff
> color sel #71aa86ff
> color sel #71aa84ff
> color sel #79aa85ff
> color sel #7aaa86ff
> color sel #85aa92ff
> color sel #89aa95ff
> color sel #8aaa96ff
> color sel #8aaa95ff
> color sel #89aa94ff
> color sel #89aa92ff
> color sel #87aa8eff
> color sel #85aa8aff
> color sel #83aa85ff
> color sel #83aa80ff
> color sel #84aa7dff
> color sel #86aa7dff
> color sel #80aa79ff
> color sel #6aaa63ff
> color sel #67aa60ff
> color sel #67aa5fff
> color sel #64aa5fff
> color sel #63aa5fff
> color sel #5faa62ff
> color sel #5faa6bff
> color sel #5faa6cff
> select clear
> select
> /A:38-39,70-74,109-110,127-131,162-164,233-234,451-457,494-495,508-514,540-543
294 atoms, 289 bonds, 39 residues, 1 model selected
> select clear
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:600
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #62aa6dff
> color sel #61aa6cff
> color sel #60aa6bff
> select /A:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #5caa69ff
> style sel stick
Changed 8 atom styles
> show sel atoms
> select /A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5caa6cff
Drag select of 2 residues
> select clear
> select /A:235
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:235
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5faa6aff
> color sel #5daa69ff
> color sel #5daa6aff
> color sel #5daa6dff
> select clear
> select /A:236
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:236
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5faa74ff
> color sel #5faa72ff
> select /A:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5daa79ff
Drag select of 2 residues
> select /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5daa76ff
> color sel #5daa77ff
> color sel #5daa79ff
> color sel #5daa7cff
> select clear
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5baa80ff
> color sel #5baa83ff
> color sel #5baa85ff
> color sel #5aaa85ff
> color sel #5aaa89ff
> color sel #57aa8aff
> color sel #53aa8aff
> color sel #52aa8dff
> color sel #4daa9aff
> color sel #4baaa4ff
> color sel #477caaff
> color sel #4777aaff
> color sel #4975aaff
> color sel #4970aaff
> color sel #4b61aaff
> color sel #4d5baaff
> color sel #4d59aaff
> color sel #4d56aaff
> color sel #5b51aaff
> color sel #8056aaff
> color sel #995aaaff
> color sel #a55baaff
> color sel #a55caaff
> color sel #a75caaff
> color sel #a75aaaff
> color sel #a757aaff
> color sel #aa57aaff
> color sel #aa57a2ff
> color sel #aa5798ff
> color sel #aa5794ff
> color sel #aa5790ff
> color sel #aa5a87ff
> color sel #aa5a85ff
> color sel #aa5984ff
> color sel #aa5274ff
> color sel #aa4c62ff
> color sel #aa495bff
> color sel #aa4759ff
> color sel #aa425aff
> color sel #aa3f5fff
> color sel #aa3a65ff
> color sel #aa3869ff
> color sel #aa3772ff
> color sel #aa3774ff
> color sel #aa377eff
> color sel #aa3785ff
> color sel #aa378bff
> color sel #aa3791ff
> color sel #aa3795ff
> color sel #aa3797ff
> color sel #aa37a0ff
> color sel #9937aaff
> color sel #8438aaff
> color sel #7f39aaff
> color sel #7f3aaaff
> color sel #803caaff
> color sel #783faaff
> color sel #7941aaff
> color sel #7743aaff
> color sel #7546aaff
> color sel #6d65aaff
> color sel #7d77aaff
> color sel #8b87aaff
> color sel #8d89aaff
> color sel #8e8aaaff
> color sel #8f8aaaff
> color sel #908aaaff
> color sel #918aaaff
> color sel #928aaaff
> color sel #938aaaff
> color sel #958aaaff
> color sel #968aaaff
> color sel #9589aaff
> color sel #9489aaff
> color sel #9087aaff
> color sel #808aaaff
> color sel #7a94aaff
> color sel #759eaaff
> color sel #6baa9aff
> color sel #65aa7bff
> color sel #6baa5dff
> color sel #89aa59ff
> color sel #aaa753ff
> color sel #aa874eff
> color sel #aa7a4bff
> color sel #aa774aff
> color sel #aa7649ff
> color sel #aa7a49ff
> color sel #aa8249ff
> color sel #aa8a49ff
> color sel #aa8f49ff
> color sel #aa9249ff
> color sel #aa9549ff
> color sel #aa9749ff
> color sel #aa9f49ff
> color sel #aaa249ff
> color sel #aaa449ff
> color sel #aaa249ff
> color sel #aa9447ff
> color sel #aa8d43ff
> color sel #aa8241ff
> color sel #aa7a3fff
> color sel #aa6a33ff
> color sel #aa622fff
> color sel #aa602cff
> color sel #aa5e2cff
> color sel #aa5a2bff
> color sel #aa552bff
> color sel #aa532bff
> color sel #aa4f2bff
> color sel #aa4e29ff
> color sel #aa4d29ff
> color sel #aa4526ff
> color sel #aa3821ff
> color sel #aa3720ff
> color sel #aa581dff
> color sel #aa7b1dff
> color sel #7eaa1fff
> color sel #3aaa21ff
> color sel #33aa21ff
> color sel #2aaa21ff
> color sel #22aa3dff
> color sel #aaffffff
> color sel #ffaa7fff
> color sel #ff55ffff
> color sel #ff557fff
> color sel #aa007fff
> color sel #005500ff
> color sel #00aa00ff
> color sel #55aa00ff
> color sel #65aa0aff
> color sel #5faa0aff
> color sel #5daa0aff
> color sel #52aa0aff
> color sel #4baa0bff
> color sel #43aa0bff
> color sel #0055ffff
> color sel #00557fff
> color sel #555500ff
> color sel #ff007fff
> color sel #ff0080ff
> color sel #fe007fff
> color sel #fd007fff
> color sel #fc007eff
> color sel #fa007dff
> color sel #f8007cff
> color sel #f5007bff
> color sel #f00078ff
> color sel #ec0076ff
> color sel #d6006bff
> color sel #c20061ff
> color sel #af0058ff
> color sel #ab0056ff
> color sel #ac0056ff
> color sel #ad0057ff
> color sel #af0058ff
Drag select of 3 residues
Drag select of 1 atoms, 2 residues, 4 bonds
> select clear
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff557fff
> color sel #ff5500ff
> color sel #ff557fff
> color sel #aaaa7fff
> color sel #aaaa00ff
> color sel #aa5500ff
> color sel #aa007fff
> color sel #aa0000ff
> color sel #55007fff
> color sel #ff007fff
> color sel #fd007fff
> color sel #f8007cff
> color sel #f7007cff
> color sel #e80074ff
> color sel #de006fff
> color sel #dd006fff
> color sel #d9006dff
> color sel #d8006cff
> color sel #d6006bff
> color sel #cf0068ff
> color sel #cb0066ff
> color sel #ca0065ff
> color sel #bf0060ff
> color sel #b00058ff
> color sel #a70054ff
> color sel #8d0047ff
> color sel #830042ff
> color sel #820041ff
> color sel #830042ff
> color sel #840042ff
> color sel #870044ff
> color sel #880044ff
> color sel #ff00ffff
> color sel #f700f7ff
> color sel #ca00caff
> color sel #b500b5ff
> color sel #990099ff
> color sel #930093ff
> color sel #910091ff
> color sel #900090ff
> color sel #8f008fff
> color sel #8d008dff
> color sel #8c008cff
> color sel #8a008aff
> color sel #730073ff
> color sel #640064ff
> color sel #560056ff
> color sel #540054ff
> color sel #550055ff
> color sel #560056ff
> color sel #590059ff
> color sel #5b005bff
> color sel #640064ff
> color sel #680068ff
> color sel #750075ff
> color sel #780078ff
> color sel #810081ff
> color sel #910091ff
> color sel #940094ff
> color sel #960096ff
> color sel #950095ff
> color sel #910091ff
> color sel #8f008fff
> color sel #8d008dff
> color sel #8c008cff
> color sel #8b008bff
> color sel #8a008aff
> color sel #870087ff
> color sel #840084ff
> color sel #860086ff
> color sel #870087ff
> select /A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #7e0287ff
> color sel byhetero
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #870885ff
> color sel #870985ff
> color sel #870a85ff
> color sel #870d87ff
> color sel #7f0f87ff
> color sel #7f1087ff
> color sel #7a1b87ff
> color sel #732587ff
> color sel #6d2b87ff
> color sel #6b3287ff
> color sel #683787ff
> color sel #623e87ff
> color sel #604a87ff
> color sel #614f87ff
> color sel #615087ff
> color sel #605087ff
> color sel #5f4f87ff
> color sel #5e4e87ff
> color sel #5e4d87ff
> color sel #5d4c87ff
> color sel #5c4b87ff
> color sel #5b4a87ff
> color sel #424987ff
> color sel #3d4a87ff
> color sel #395187ff
> color sel #385787ff
> color sel #375987ff
> color sel #326987ff
> color sel #2f7787ff
> color sel #2f7887ff
> color sel #2f8387ff
> color sel #2f8687ff
> color sel #2f8087ff
> color sel #2e8087ff
> color sel #2e7b87ff
> color sel #2d7887ff
> color sel #2c7887ff
> color sel #2c7b87ff
> color sel #2c8287ff
> color sel #2c8587ff
> color sel byhetero
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #287787ff
> color sel byhetero
> select /A:422
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:422
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #267f87ff
> color sel #277f87ff
> color sel #277d87ff
> color sel #287d87ff
> color sel #287a87ff
> show sel atoms
> color sel byhetero
> select clear
> select :AV0
69 atoms, 72 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 69 atom styles
> select add /A:58
77 atoms, 79 bonds, 2 residues, 1 model selected
> select add /A:139
85 atoms, 86 bonds, 3 residues, 1 model selected
> select add /A:422
93 atoms, 93 bonds, 4 residues, 1 model selected
> hbonds sel reveal true
17 hydrogen bonds found
> style sel stick
Changed 93 atom styles
> ~hbonds
> select clear
> select /A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:422@CA
1 atom, 1 residue, 1 model selected
> select add /A:139
9 atoms, 7 bonds, 2 residues, 1 model selected
> select add /A:58
17 atoms, 14 bonds, 3 residues, 1 model selected
> color sel #aa00ffff
> color sel #550000ff
> color sel #55007fff
> color sel #555500ff
> color sel #ff5500ff
> color sel #00aaffff
> color sel #039effff
> color sel #03a7ffff
> color sel #03afffff
> color sel #0be7ffff
> color sel #23ffcfff
> color sel #33ffccff
> color sel #3effc8ff
> color sel #4bffc9ff
> color sel #55ffccff
> color sel #60ffcfff
> color sel #61ffd0ff
> color sel #75ffd6ff
> color sel #83ffdaff
> color sel #8cffddff
> color sel #99ffe6ff
> color sel #a6ffecff
> color sel #b2fff0ff
> color sel #b3fff2ff
> color sel #b0fff2ff
> color sel #a4fff7ff
> color sel #a2fff7ff
> color sel #94fff8ff
> color sel #92fff8ff
> color sel #87ffffff
> color sel #83ffffff
> color sel #73f8ffff
> color sel #6ef3ffff
> color sel #6cf3ffff
> color sel #60eaffff
> color sel #58e9ffff
> color sel #57e9ffff
> color sel #54e8ffff
> color sel #45ecffff
> color sel #42ecffff
> color sel #42efffff
> color sel #37ffffff
> color sel #34fff8ff
> color sel #33fff8ff
> color sel #31fff8ff
> color sel #30fff8ff
> color sel #2efff8ff
> color sel #2bfff8ff
> color sel #2bffffff
> color sel #2bfbffff
> color sel #29edffff
> color sel #22e2ffff
> color sel #20d6ffff
> color sel #1ccaffff
> color sel #1ac2ffff
> color sel #18aeffff
> color sel #14a1ffff
> color sel #1499ffff
> color sel #1399ffff
> color sel #1097ffff
> color sel #0c8effff
> color sel #0b89ffff
> color sel #0a89ffff
> color sel #0a80ffff
> color sel #0a78ffff
> color sel #0a74ffff
> color sel #0a78ffff
> color sel #0a80ffff
> color sel #0b81ffff
> color sel #0c81ffff
> color sel #0c8affff
> color sel #0c8effff
> color sel #0c9effff
> color sel #0e9fffff
> color sel #0fa3ffff
> color sel #11acffff
> color sel #11b4ffff
> color sel #11b8ffff
> color sel #10b7ffff
> color sel #0fb7ffff
> color sel #0eb7ffff
> color sel #0cb6ffff
> color sel #0bb6ffff
> color sel #0bbeffff
> color sel #0bc6ffff
> color sel #0bd2ffff
> color sel byhetero
> hbonds sel reveal true
7 hydrogen bonds found
> ~hbonds
> select add /A:801@C3
18 atoms, 15 bonds, 4 residues, 1 model selected
> select ~sel
5491 atoms, 5603 bonds, 1 pseudobond, 716 residues, 3 models selected
> select clear
> select :AV0
69 atoms, 72 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
12 hydrogen bonds found
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show "Side View"
> view orient
> graphics silhouettes true
> view sel
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select /A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:236
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add /A:235
31 atoms, 30 bonds, 3 residues, 1 model selected
> select add /A:173
39 atoms, 37 bonds, 4 residues, 1 model selected
> select add /A:169
46 atoms, 43 bonds, 5 residues, 1 model selected
> select add /A:166
54 atoms, 50 bonds, 6 residues, 1 model selected
> select add /A:447
66 atoms, 62 bonds, 7 residues, 1 model selected
> select add /A:440
77 atoms, 73 bonds, 8 residues, 1 model selected
> contacts sel select true makePseudobonds false
111 contacts
> select clear
> select /A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:139
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /A:422
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /A:166
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add /A:447
44 atoms, 40 bonds, 5 residues, 1 model selected
> select add /A:169
51 atoms, 46 bonds, 6 residues, 1 model selected
> select add /A:173
59 atoms, 53 bonds, 7 residues, 1 model selected
> select add /A:236
70 atoms, 64 bonds, 8 residues, 1 model selected
> select add /A:177
78 atoms, 71 bonds, 9 residues, 1 model selected
> select add /A:440
89 atoms, 82 bonds, 10 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label height 1
> select clear
> save C:\Users\fern0096/Desktop\image1.png supersample 3
> save C:\Users\fern0096/Desktop\image2.png supersample 3
> save C:\Users\fern0096/Desktop\image3.png supersample 3
> save C:\Users\fern0096/Desktop\image4.png supersample 3
> save C:\Users\fern0096/Desktop\image5.png supersample 3
> save C:\Users\fern0096/Desktop\image6.png supersample 3
> transparency 50
> save C:\Users\fern0096/Desktop\image7.png supersample 3
> select :AV0
69 atoms, 72 bonds, 9 pseudobonds, 1 residue, 2 models selected
> style sel sphere
Changed 69 atom styles
> select clear
> save C:\Users\fern0096/Desktop\image8.png supersample 3
> save C:\Users\fern0096/Desktop\image9.png supersample 3
> save C:\Users\fern0096/Desktop\image10.png supersample 3
> save C:\Users\fern0096/Desktop\image11.png supersample 3
> save C:\Users\fern0096/Desktop\image12.png supersample 3
> save "C:/Users/fern0096/Desktop/CHEM5760/Binding site.cxs" includeMaps true
——— End of log from Thu Oct 23 03:11:07 2025 ———
> view name session-start
opened ChimeraX session
> ui mousemode right "translate selected models"
> select add /A:236
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:173
19 atoms, 20 bonds, 2 residues, 1 model selected
> select add /A:447@CG
20 atoms, 20 bonds, 3 residues, 1 model selected
> select add /A:166
28 atoms, 27 bonds, 4 residues, 1 model selected
> select add /A:440
39 atoms, 38 bonds, 5 residues, 1 model selected
> select add /A:169
46 atoms, 44 bonds, 6 residues, 1 model selected
> select up
51 atoms, 45 bonds, 8 residues, 1 model selected
> select up
77 atoms, 74 bonds, 8 residues, 1 model selected
> mlp sel
Map values for surface "7nvh_A SES surface": minimum -29.12, mean -1.997,
maximum 25.85
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide sel surfaces
> select clear
> select add /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add /A:440
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add /A:169
30 atoms, 29 bonds, 3 residues, 2 models selected
> select add /A:173
38 atoms, 36 bonds, 4 residues, 2 models selected
> select add /A:550
46 atoms, 43 bonds, 5 residues, 2 models selected
> select subtract /A:550
38 atoms, 36 bonds, 4 residues, 2 models selected
> select add /A:235
50 atoms, 49 bonds, 5 residues, 2 models selected
> select add /A:236@CD2
51 atoms, 49 bonds, 6 residues, 2 models selected
> select add /A:695
59 atoms, 56 bonds, 7 residues, 2 models selected
> select subtract /A:695
51 atoms, 49 bonds, 6 residues, 2 models selected
> select up
55 atoms, 50 bonds, 8 residues, 2 models selected
> select up
77 atoms, 74 bonds, 8 residues, 2 models selected
> select clear
> hide cartoons
> select clear
> select /A:169@CB
1 atom, 1 residue, 1 model selected
> select clear
> show sel cartoons
> select clear
> show cartoons
> select /A:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:177
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add /A:236
27 atoms, 25 bonds, 3 residues, 2 models selected
Drag select of 2 residues
> select clear
> select /A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:236
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add /A:173
27 atoms, 25 bonds, 3 residues, 2 models selected
> select add /A:440
38 atoms, 36 bonds, 4 residues, 2 models selected
> select add /A:801@OBZ
39 atoms, 36 bonds, 5 residues, 2 models selected
> select subtract /A:801@OBZ
38 atoms, 37 bonds, 4 residues, 2 models selected
> select add /A:447@CG
39 atoms, 37 bonds, 5 residues, 2 models selected
> select add /A:166
47 atoms, 48 bonds, 6 residues, 2 models selected
> select add /A:67
51 atoms, 54 bonds, 7 residues, 2 models selected
> select subtract /A:67
47 atoms, 51 bonds, 6 residues, 2 models selected
> select add /A:67
51 atoms, 55 bonds, 7 residues, 2 models selected
> select subtract /A:67
47 atoms, 52 bonds, 6 residues, 2 models selected
> select add /A:169
54 atoms, 58 bonds, 7 residues, 2 models selected
> ui tool show Contacts
[Repeated 1 time(s)]
> contacts sel restrict #1:AV0 intraRes true ignoreHiddenModels true color
> #ff00ff
11 contacts
> view matrix models #1,1,0,0,0.74841,0,1,0,4.0992,0,0,1,-5.829
> view matrix models #1,1,0,0,0.96162,0,1,0,4.1479,0,0,1,-4.0115
> select clear
> select /A:801@CCR
1 atom, 1 residue, 1 model selected
> select up
69 atoms, 72 bonds, 1 residue, 1 model selected
> select up
5509 atoms, 5627 bonds, 718 residues, 1 model selected
> select clear
> select /A:801@CCR
1 atom, 1 residue, 1 model selected
> select up
69 atoms, 72 bonds, 1 residue, 1 model selected
> name frozen LMNG sel
> select clear
> select LMNG
69 atoms, 72 bonds, 9 pseudobonds, 1 residue, 2 models selected
> select clear
[Repeated 1 time(s)]
> select /A:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:236
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:236
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add /A:235
31 atoms, 30 bonds, 3 residues, 2 models selected
> select add /A:173
39 atoms, 37 bonds, 4 residues, 2 models selected
> select add /A:169
46 atoms, 43 bonds, 5 residues, 2 models selected
> select add /A:166
54 atoms, 50 bonds, 6 residues, 2 models selected
> select add /A:440
65 atoms, 61 bonds, 7 residues, 2 models selected
> select add /A:447
77 atoms, 73 bonds, 8 residues, 2 models selected
> contacts sel overlapCutoff 0.19999999999999998 select true makePseudobonds
> false
1 contacts
> contacts sel overlapCutoff -0.9999999999999999 select true makePseudobonds
> false
16 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -1.2 intraRes true
> ignoreHiddenModels true color #ff0ae7
13 contacts
> select add /A:177
25 atoms, 7 bonds, 8 residues, 2 models selected
> select add /A:173
33 atoms, 14 bonds, 9 residues, 2 models selected
> select add /A:169
40 atoms, 20 bonds, 10 residues, 2 models selected
> select add /A:166
48 atoms, 27 bonds, 11 residues, 2 models selected
> select add /A:440
59 atoms, 38 bonds, 12 residues, 2 models selected
> select subtract /A:38
58 atoms, 38 bonds, 11 residues, 2 models selected
> select add /A:38
65 atoms, 44 bonds, 12 residues, 2 models selected
> select subtract /A:38
58 atoms, 38 bonds, 11 residues, 2 models selected
> select subtract /A:39
56 atoms, 38 bonds, 10 residues, 2 models selected
> select subtract /A:234
53 atoms, 38 bonds, 9 residues, 2 models selected
> select subtract /A:306
51 atoms, 38 bonds, 8 residues, 2 models selected
> select add /A:447
63 atoms, 50 bonds, 9 residues, 2 models selected
> select subtract /A:801@CAY
62 atoms, 50 bonds, 8 residues, 2 models selected
Drag select of 7 atoms, 5 bonds
> select add /A:801@CCJ
66 atoms, 50 bonds, 10 residues, 2 models selected
> select subtract /A:801@CBL
65 atoms, 50 bonds, 10 residues, 2 models selected
> select add /A:801@CBT
66 atoms, 50 bonds, 10 residues, 2 models selected
> select subtract /A:801@CBT
65 atoms, 50 bonds, 10 residues, 2 models selected
> select add /A:801@CBQ
66 atoms, 50 bonds, 10 residues, 2 models selected
> select subtract /A:801@CBQ
65 atoms, 50 bonds, 10 residues, 2 models selected
> select add /A:422@CB
66 atoms, 50 bonds, 10 residues, 2 models selected
> select add /A:422@CG1
67 atoms, 50 bonds, 10 residues, 2 models selected
> select subtract /A:801@CCJ
66 atoms, 50 bonds, 10 residues, 2 models selected
> select subtract /A:422
63 atoms, 48 bonds, 9 residues, 2 models selected
> select subtract /A:235@CA
62 atoms, 48 bonds, 9 residues, 2 models selected
> select add /A:305
66 atoms, 54 bonds, 10 residues, 2 models selected
> select subtract /A:305
62 atoms, 51 bonds, 9 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -2.0000000000000004 intraRes true
> ignoreHiddenModels true color #ff0ae7
140 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -1.3999999999999995 intraRes true
> ignoreHiddenModels true color #ff0ae7
85 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.9999999999999997 intraRes true
> ignoreHiddenModels true color #ff0ae7
55 contacts
> select clear
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /A:166
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add /A:173
23 atoms, 20 bonds, 3 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.7000000000000001 intraRes true
> ignoreHiddenModels true color #ff0ae7
19 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.9999999999999999 intraRes true
> ignoreHiddenModels true color #ff0ae7
42 contacts
> select add /A:440
34 atoms, 31 bonds, 4 residues, 2 models selected
> select add /A:447
46 atoms, 43 bonds, 5 residues, 2 models selected
> select add /A:236
57 atoms, 54 bonds, 6 residues, 2 models selected
> select add /A:177
65 atoms, 61 bonds, 7 residues, 2 models selected
> select add /A:235
77 atoms, 73 bonds, 8 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -1.0 intraRes true
> ignoreHiddenModels true color #ff0ae7
64 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.8 intraRes true
> ignoreHiddenModels true color #ff0ae7
44 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.7000000000000001 intraRes true
> ignoreHiddenModels true color #ff0ae7
33 contacts
> ui tool show Contacts
> contacts sel restrict #1:AV0 overlapCutoff -0.6 intraRes true
> ignoreHiddenModels true color #ff0ae7
30 contacts
> select clear
> select helix
3851 atoms, 3898 bonds, 506 residues, 1 model selected
> transparency sel 50 target r
> transparency sel 80 target r
> select helix
3851 atoms, 3898 bonds, 506 residues, 1 model selected
> select coil
1295 atoms, 1300 bonds, 1 pseudobond, 172 residues, 2 models selected
> transparency sel 80 target r
> transparency sel 80 target c
> select strand
294 atoms, 289 bonds, 39 residues, 1 model selected
> transparency sel 80 target s
> select clear
> save "C:/Users/fern0096/Desktop/CHEM5760/Binding site 2.cxs"
> close session
> open 7NVH format mmcif fromDatabase pdb
7nvh title:
Cryo-EM structure of the mycolic acid transporter MmpL3 from M. tuberculosis
[more info...]
Chain information for 7nvh #1
---
Chain | Description | UniProt
A | Trehalose monomycolate exporter MmpL3 | MMPL3_MYCTU 1-753
Non-standard residues in 7nvh #1
---
AV0 — Lauryl Maltose Neopentyl Glycol (2,2-didecylpropane-1,3-bis-b-D-
maltopyranoside; 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranoside)
19 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 7NVH format mmcif fromDatabase pdb
7nvh title:
Cryo-EM structure of the mycolic acid transporter MmpL3 from M. tuberculosis
[more info...]
Chain information for 7nvh #2
---
Chain | Description | UniProt
A | Trehalose monomycolate exporter MmpL3 | MMPL3_MYCTU 1-753
Non-standard residues in 7nvh #2
---
AV0 — Lauryl Maltose Neopentyl Glycol (2,2-didecylpropane-1,3-bis-b-D-
maltopyranoside; 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-
glucopyranoside)
19 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open P9WJV5 fromDatabase uniprot associate #2/A
Error from UniProt web server while checking job status: HTTP Error 400:
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.
> select #2/A:1-753
5440 atoms, 5555 bonds, 1 pseudobond, 717 residues, 2 models selected
> open P9WJV5 fromDatabase uniprot associate #2/A
Error from UniProt web server while checking job status: HTTP Error 400:
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.
> open P9WJV5 fromDatabase uniprot associate #2/A
Error from UniProt web server while checking job status: HTTP Error 400:
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.
> select clear
> open P9WJV5 fromDatabase uniprot associate #1/A
Error from UniProt web server while checking job status: HTTP Error 400:
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.
> hide #!2 models
> open P9WJV5 fromDatabase uniprot associate #1/A
Error from UniProt web server while checking job status: HTTP Error 400:
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.
OpenGL version: 3.3.0 - Build 32.0.101.6078
OpenGL renderer: Intel(R) Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Latitude 5450
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 16,597,598,208
MaxProcessMemory: 137,438,953,344
CPU: 14 Intel(R) Core(TM) Ultra 5 125U
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
File attachment: Screenshot (114).png
Screenshot (114).png
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