![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#7466 closed defect (fixed)
Coloring surface: self.vertices is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-124-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open fuzja.pdb
Summary of feedback from opening fuzja.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-06-02 Time 15:26:10 CEST +0200 (1654176370.09 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/ania_k/Phenix_output/resolutions-
diff/195A/fuzja_1_18_I.mtz
45 messages similar to the above omitted
Chain information for fuzja.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
Drag select of 534 atoms, 843 residues, 2 pseudobonds, 458 bonds
> hide sel atoms
> select clear
Drag select of 844 residues, 2 pseudobonds
> color (#!1 & sel) dark gray
> select clear
> lighting soft
> graphics silhouettes true
> select #1/A :85-129 :352-398
756 atoms, 769 bonds, 92 residues, 1 model selected
> color sel orange red
> select #1/B :85-129 :352-398
752 atoms, 765 bonds, 92 residues, 1 model selected
> color sel yellow
> select clear
> surface ::name="SAM" resolution 4
2 Gaussian surfaces, threshold level 0.348
> surface ::name="SAM" resolution 4 transparency 50
2 Gaussian surfaces, threshold level 0.348
> surface ::name="SAM" resolution 4 transparency 50
2 Gaussian surfaces, threshold level 0.348
> color bypolymer
Surface #1.2 does not have atom patches, cannot color by atom
> color bychain
Surface #1.2 does not have atom patches, cannot color by atom
> color byhetero
> surface ::name="SAM" resolution 4 transparency 100
2 Gaussian surfaces, threshold level 0.348
> surface ::name="SAM" resolution 4 transparency 20
2 Gaussian surfaces, threshold level 0.348
> surface ::name="SAM" resolution 4 transparency 0
2 Gaussian surfaces, threshold level 0.348
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel hot pink
> color sel medium blue
> ui tool show "Color Actions"
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel #3465a4ff
> color sel #204a87ff
> color sel #3465a4ff
> surface ::name="SAM" resolution 3
2 Gaussian surfaces, threshold level 0.640 - 0.643
> surface ::name="SAM" resolution 2
2 Gaussian surfaces, threshold level 1.970 - 1.971
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> surface ::name="SAM" resolution 3.0
2 Gaussian surfaces, threshold level 0.640 - 0.643
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> color sel purple
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #bf5b5bff
> color sel #e46d6dff
> color sel #e47171ff
> color sel #e67272ff
> color sel #e68989ff
> color sel #e69393ff
> color sel #e69999ff
> color sel #e89a9aff
> color sel #e89c9cff
> color sel #e99d9dff
> color sel #e99e9eff
> color sel #ea9e9eff
> color sel #eaa7a7ff
> color sel #eda9a9ff
> color sel #edb6b6ff
> color sel #f2babaff
> color sel #f2c3c3ff
> color sel #f2c7c7ff
> color sel #f4c9c9ff
> color sel #f4cacaff
> color sel #f3c9c9ff
> color sel #f3bbbbff
> color sel #edb7b7ff
> color sel #eda5a5ff
> color sel #efa6a6ff
> color sel #efa5a5ff
> color sel #efa4a4ff
> color sel #f0a5a5ff
[Repeated 1 time(s)]
> color sel #f1a6a6ff
> color sel #f1adadff
> color sel #f1b4b4ff
> color sel #f1b8b8ff
> color sel #f1bcbcff
> color sel #f2bdbdff
> color sel #f2bebeff
> color sel #f2bfbfff
> color sel #f2c0c0ff
> color sel #f3c1c1ff
> color sel #f3c3c3ff
> color sel #f3c5c5ff
> color sel #f3c6c6ff
> color sel #f2c5c5ff
> color sel #f2c6c6ff
> color sel #f3c7c7ff
> color sel #f3d3d3ff
> color sel #f7d6d6ff
> color sel #f7dbdbff
> color sel #f7dfdfff
> color sel #f7e4e4ff
> color sel #f9e6e6ff
> color sel #f9ebebff
> color sel #fbededff
> color sel #f9ebebff
> color sel #f9eaeaff
> color sel #f8e9e9ff
> color sel #f8e8e8ff
> color sel #f8d6d6ff
> color sel #f7d5d5ff
> color sel #f7ceceff
> color sel #f7cdcdff
> color sel #f7cacaff
> color sel #f6c9c9ff
> color sel #f5c9c9ff
> color sel #f4c8c8ff
> color sel #f4cacaff
> color sel #f0c6c6ff
> color sel #ecc3c3ff
> color sel #ebc3c3ff
> color sel #ebc2c2ff
> color sel #ebaeaeff
> color sel #f1b3b3ff
> color sel #f1a7a7ff
> color sel #f5aaaaff
> color sel #f59e9eff
> color sel #f79f9fff
> color sel #f79191ff
> color sel #f78888ff
> color sel #f58787ff
> color sel #f57979ff
> color sel #f37878ff
> color sel #f36e6eff
> color sel #f16d6dff
> color sel #f16c6cff
> color sel #f26c6cff
> color sel #f26f6fff
> color sel #f46f6fff
> color sel #f48888ff
> color sel #f68989ff
> color sel #f69d9dff
> color sel #f89f9fff
> color sel #f8ababff
> color sel #fcaeaeff
> color sel #fcb3b3ff
> color sel #fcb7b7ff
> color sel #fcb9b9ff
> color sel #fcbbbbff
> color sel #fcbabaff
> color sel #fcbbbbff
> color sel #fbbabaff
> color sel #fababaff
> color sel #fabbbbff
> color sel #f7babaff
[Repeated 1 time(s)]
> color sel #f4b8b8ff
> color sel #f4b9b9ff
> color sel #f2b7b7ff
[Repeated 2 time(s)]
> select #1/A :85-129 :352-398
756 atoms, 769 bonds, 92 residues, 1 model selected
> color sel orange red
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) #fce94fff
> color (#!1 & sel) #bfba40ff
[Repeated 1 time(s)]
> color (#!1 & sel) #cbc544ff
> color (#!1 & sel) #cbc64fff
> color (#!1 & sel) #d6d053ff
> color (#!1 & sel) #d6d167ff
> color (#!1 & sel) #ded96aff
> color (#!1 & sel) #deda7cff
> color (#!1 & sel) #e6e181ff
> color (#!1 & sel) #e6e189ff
> color (#!1 & sel) #e9e58bff
> color (#!1 & sel) #e9e597ff
> color (#!1 & sel) #ece99aff
> color (#!1 & sel) #ece9a1ff
> color (#!1 & sel) #f0eca4ff
> color (#!1 & sel) #f0eca7ff
> color (#!1 & sel) #f1eda8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f1eda9ff
> color (#!1 & sel) #f1eeafff
> color (#!1 & sel) #f2efb0ff
> color (#!1 & sel) #f2f0b6ff
> color (#!1 & sel) #f2f0b7ff
> color (#!1 & sel) #f1efb7ff
[Repeated 2 time(s)]
> select #1/B :85-129 :352-398
752 atoms, 765 bonds, 92 residues, 1 model selected
> color sel yellow
> color sel #c4a000ff
> color sel #bdbf40ff
> color sel #b8bf40ff
> color sel #b5bf40ff
> color sel #b0bf40ff
> color sel #aebf40ff
> color sel #abbf40ff
> color sel #a8bf40ff
> color sel #a6bf40ff
> color sel #a3bf40ff
> color sel #a6bf40ff
> color sel #a8bf40ff
> color sel #abbf40ff
> color sel #aebf40ff
> color sel #b0bf40ff
> color sel #b5bf40ff
> color sel #b8bf40ff
> color sel #babf40ff
> color sel #bdbf40ff
> color sel #bfbf40ff
> color sel #bfbf33ff
> color sel #c4c434ff
> color sel #c1c434ff
> color sel #c1c42cff
> color sel #babd2aff
> color sel #b9bd16ff
> color sel #b8bb16ff
> color sel #b8bb0fff
> color sel #b6b90fff
> color sel #b6b90dff
> color sel #b4b80dff
> color sel #b4b80cff
> color sel #b5b80cff
> color sel #b5b80aff
> color sel #c4c80bff
> color sel #c4c809ff
> color sel #ccd00aff
> color sel #ccd008ff
> color sel #d0d408ff
> color sel #d4d809ff
> color sel #d5da09ff
> color sel #d5d909ff
> color sel #d5d90aff
> color sel #ccd00aff
> color sel #ccd00cff
> color sel #c4c80cff
> color sel #c4c80dff
> color sel #c1c40cff
> color sel #c1c40eff
> color sel #c9cd0eff
> color sel #c9cd0fff
> color sel #c9cd1aff
> color sel #c4c819ff
> color sel #c4c81fff
> color sel #c2c51fff
> color sel #c2c51eff
> color sel #c1c41eff
> color sel #c1c40eff
> color sel #c9cd0fff
> color sel #c9cd10ff
> color sel #c9cd12ff
> color sel #c7cb12ff
> color sel #c8cb18ff
> color sel #c4c817ff
> color sel #c4c818ff
> color sel #c8c718ff
> color sel #c5c818ff
> color sel #b6c818ff
> color sel #afc818ff
> color sel #a8c818ff
> color sel #9dc818ff
> color sel #96c818ff
> color sel #7dc818ff
> color sel #5ac818ff
> color sel #36c818ff
> color sel #18c81eff
> color sel #18c842ff
> color sel #18c850ff
> color sel #18c87bff
> color sel #18c89fff
> color sel #18c8adff
> color sel #18c8b1ff
> color sel #18c8adff
> color sel #18c8a9ff
> color sel #18c862ff
> color sel #3dc818ff
> color sel #76c818ff
> color sel #8cc818ff
> color sel #a1c818ff
> color sel #b6c818ff
> color sel #c8c418ff
> color sel #c8b918ff
> color sel #c8ab18ff
> color sel #c89218ff
> color sel #c88e18ff
> color sel #c89218ff
> color sel #c89518ff
> color sel #c89918ff
> color sel #c8a018ff
> color sel #c8a718ff
> color sel #c8b518ff
> color sel #c8c718ff
> color sel #c5c818ff
> color sel #c1c818ff
> color sel #c5c818ff
> color sel #c8b918ff
> color sel #c8b218ff
> color sel #c8a718ff
> color sel #c8a318ff
> color sel #c8a018ff
> color sel #c89c18ff
> color sel #c8a018ff
> color sel #c8a318ff
> color sel #c8a718ff
> color sel #c1c818ff
> color sel #acc818ff
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) #bf8840ff
> color (#!1 & sel) #bf9040ff
> color (#!1 & sel) #bf9840ff
> color (#!1 & sel) #bfb240ff
> color (#!1 & sel) #bfb440ff
> color (#!1 & sel) #bfb740ff
> color (#!1 & sel) #62bf40ff
> color (#!1 & sel) #40bf51ff
> color (#!1 & sel) #40bf7bff
> color (#!1 & sel) #40bf9aff
> color (#!1 & sel) #40bfa4ff
> color (#!1 & sel) #40bfa9ff
> color (#!1 & sel) #40bfaeff
> color (#!1 & sel) #40bfb4ff
> color (#!1 & sel) #40bfb6ff
> color (#!1 & sel) #40bfbeff
> color (#!1 & sel) #40b4bfff
> color (#!1 & sel) #40aebfff
> color (#!1 & sel) #40acbfff
> color (#!1 & sel) #40a9bfff
> color (#!1 & sel) #40a7bfff
> color (#!1 & sel) #409abfff
> color (#!1 & sel) #4092bfff
> color (#!1 & sel) #408dbfff
> color (#!1 & sel) #408fbfff
> color (#!1 & sel) #40a9bfff
> color (#!1 & sel) #40bfacff
> color (#!1 & sel) #40bf9cff
> color (#!1 & sel) #40bf9aff
> color (#!1 & sel) #40bf94ff
> color (#!1 & sel) #40bf8fff
> color (#!1 & sel) #40bf7bff
> color (#!1 & sel) #40bf6bff
> color (#!1 & sel) #40bf61ff
> color (#!1 & sel) #40bf59ff
> color (#!1 & sel) #40bf56ff
> color (#!1 & sel) #40bf54ff
> color (#!1 & sel) #40bf56ff
> color (#!1 & sel) #40bf94ff
> color (#!1 & sel) #4094bfff
> color (#!1 & sel) #4075bfff
> color (#!1 & sel) #4061bfff
> color (#!1 & sel) #4049bfff
> color (#!1 & sel) #4044bfff
> color (#!1 & sel) #5340bfff
> color (#!1 & sel) #6240bfff
> color (#!1 & sel) #9640bfff
> color (#!1 & sel) #b540bfff
> color (#!1 & sel) #bd40bfff
> color (#!1 & sel) #bf40bcff
> color (#!1 & sel) #bf40a7ff
> color (#!1 & sel) #bf4088ff
> color (#!1 & sel) #bf4074ff
> color (#!1 & sel) #bf4052ff
> color (#!1 & sel) #bf4048ff
> color (#!1 & sel) #bf4045ff
> color (#!1 & sel) #bf4048ff
> color (#!1 & sel) #bf404dff
> color (#!1 & sel) #ae40bfff
> color (#!1 & sel) #8e40bfff
> color (#!1 & sel) #5540bfff
> color (#!1 & sel) #4078bfff
> color (#!1 & sel) #40acbfff
> color (#!1 & sel) #40bfa9ff
> color (#!1 & sel) #40bfa1ff
> color (#!1 & sel) #40bf9fff
> color (#!1 & sel) #40bfa1ff
> color (#!1 & sel) #40bfaeff
> color (#!1 & sel) #405ebfff
> color (#!1 & sel) #8440bfff
> color (#!1 & sel) #9940bfff
> color (#!1 & sel) #9b40bfff
> color (#!1 & sel) #9e40bfff
> color (#!1 & sel) #a140bfff
> color (#!1 & sel) #a640bfff
> color (#!1 & sel) #ba40bfff
> color (#!1 & sel) #bf40a0ff
> color (#!1 & sel) #bf4076ff
> color (#!1 & sel) #bf405aff
> color (#!1 & sel) #bf4057ff
> color (#!1 & sel) #bf4054ff
> color (#!1 & sel) #bf4052ff
> color (#!1 & sel) #bf404fff
[Repeated 2 time(s)]
> color sel light gray
> color sel gray
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select #1/B :85-129 :352-398
752 atoms, 765 bonds, 92 residues, 1 model selected
> color sel dim gray
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #729fcfff
> color sel #40a7bfff
> color sel #40a4bfff
> color sel #4092bfff
> color sel #4087bfff
> color sel #4082bfff
> color sel #4080bfff
> color sel #407dbfff
> color sel #447fbfff
> color sel #3f77b3ff
> color sel #4479b3ff
> color sel #457bb6ff
> color sel #5f89b6ff
> color sel #618bb9ff
> color sel #6f93b9ff
> color sel #7194b9ff
> color sel #7295bbff
> color sel #7697bbff
> color sel #7a99bbff
> color sel #7b9bbdff
> color sel #7c9bbdff
> color sel #7c9cbeff
> color sel #7e9ec0ff
> color sel #83a3c7ff
> color sel #84a4c7ff
> color sel #8badd1ff
> color sel #8cadd1ff
> color sel #90b2d6ff
> color sel #91b2d6ff
> color sel #93b5daff
> color sel #92b4d8ff
> color sel #92b3d7ff
[Repeated 1 time(s)]
> color sel #91b2d5ff
> color sel #91b1d5ff
> color sel #8fb0d5ff
> color sel #8eafd3ff
> color sel #88acd3ff
> color sel #83a6ccff
> color sel #7ea3ccff
> color sel #7b9fc7ff
> color sel #799fc7ff
> color sel #789dc5ff
[Repeated 1 time(s)]
> color sel #779cc4ff
> color sel #769bc4ff
> color sel #759bc3ff
> color sel #769bc4ff
> color sel #84a3c4ff
> color sel #89a8caff
> color sel #8eabcaff
> color sel #8fadccff
> color sel #91adccff
> color sel #8fadccff
> color sel #8faccbff
> color sel #8baacbff
> color sel #88a7c8ff
> color sel #85a5c8ff
> color sel #83a3c5ff
> color sel #81a2c5ff
> color sel #80a0c4ff
> color sel #80a1c4ff
[Repeated 2 time(s)]
> select #1/A :85-129 :352-398
756 atoms, 769 bonds, 92 residues, 1 model selected
> color sel cornflower blue
> color sel medium blue
> color sel #204a87ff
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #406ebfff
> color sel #7992bfff
> color sel #677ca2ff
> color sel #6e81a2ff
> color sel #7285a8ff
> color sel #7a8ba8ff
> color sel #8091b0ff
> color sel #8595b0ff
> color sel #8898b4ff
> color sel #8a99b4ff
> color sel #8b9ab6ff
> color sel #8a9ab6ff
> color sel #8b9bb7ff
> color sel #8c9bb8ff
> color sel #8b9bb8ff
> color sel #8c9cb8ff
> color sel #92a3c1ff
> color sel #91a2c1ff
> color sel #9db0d2ff
> color sel #9cafd2ff
> color sel #a4b8dcff
> color sel #a2b7dcff
> color sel #a7bde3ff
> color sel #a6bce3ff
> color sel #a8bee6ff
[Repeated 1 time(s)]
> color sel #a7bde6ff
> color sel #a7bee6ff
> color sel #9eb8e6ff
> color sel #99b5e6ff
> color sel #9db9ecff
> color sel #9ab7ecff
> color sel #9cbaf0ff
> color sel #9ab9f0ff
> color sel #9cbbf2ff
> color sel #9cbcf3ff
> color sel #9dbcf4ff
> color sel #9fbef7ff
> color sel #9fbff7ff
> color sel #a0bff7ff
> color sel #a6c3f7ff
> color sel #a9c5f7ff
> color sel #a8c4f7ff
[Repeated 1 time(s)]
> color sel #a7c3f6ff
> color sel #a6c3f6ff
> color sel #a6c2f5ff
> color sel #a6c3f5ff
> color sel #a6c2f4ff
> color sel #a7c2f4ff
> color sel #a6c2f3ff
> color sel #a4bff0ff
> color sel #a5c0f1ff
[Repeated 2 time(s)]
> select clear
> select #1/A :85-129 :352-398
756 atoms, 769 bonds, 92 residues, 1 model selected
> color sel medium blue
> color sel cornflower blue
> color sel #204a87ff
> select clear
[Repeated 1 time(s)]
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #bf404fff
> color sel #bf6868ff
> color sel #d47373ff
> color sel #d48080ff
> color sel #d49999ff
> color sel #dc9f9fff
> color sel #dcababff
> color sel #e1afafff
> color sel #e1b1b1ff
> color sel #e1b2b2ff
> color sel #e0b1b1ff
[Repeated 1 time(s)]
> color sel #e09d9dff
> color sel #e29e9eff
> color sel #e29292ff
> color sel #e69494ff
> color sel #e69191ff
> color sel #e89393ff
> color sel #e88f8fff
> color sel #e99090ff
> color sel #e98f8fff
> color sel #ea8f8fff
[Repeated 1 time(s)]
> color sel #eb8f8fff
> color sel #eb9090ff
> color sel #ec9191ff
> color sel #ecb2b2ff
> color sel #f0b5b5ff
[Repeated 1 time(s)]
> color sel #f1b6b6ff
> color sel #f1b7b7ff
> color sel #f1b6b6ff
> color sel #f2b6b6ff
> color sel #f2b5b5ff
> color sel #f4b6b6ff
[Repeated 2 time(s)]
> select #1/A :85-129 :352-398
756 atoms, 769 bonds, 92 residues, 1 model selected
> color sel #bf404fff
> select clear
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> color sel medium blue
> color sel blue
> ui tool show "Color Actions"
> color sel #204a87ff
> color sel #3465a4ff
> color sel #729fcfff
> color sel #3465a4ff
> color sel #edd400ff
> color sel #fce94fff
> color sel #edd400ff
> color sel #c4a000ff
> color sel #edd400ff
> color sel lime
> color sel cyan
[Repeated 1 time(s)]
> color sel #fce94fff
> color sel #8ae234ff
> color sel #fcaf3eff
> color sel #ef2929ff
> color sel #cc0000ff
> color sel #ce5c00ff
> color sel #c4a000ff
> color sel #b0bf40ff
> color sel #b3bf40ff
> color sel #b5bf40ff
> color sel #8ebf40ff
> color sel #43bf40ff
> color sel #40bfb9ff
> color sel #40acbfff
> color sel #4097bfff
> color sel #4092bfff
> color sel #408fbfff
> color sel #407dbfff
> color sel #4068bfff
> color sel #4059bfff
> color sel #405ebfff
> color sel #4087bfff
> color sel #4097bfff
> color sel #40acbfff
> color sel #40b9bfff
> color sel #40bbbfff
> color sel #55bcbfff
> color sel #5fd2d5ff
> color sel #62d2d5ff
> color sel #5ec9ccff
> color sel #66c9ccff
> color sel #5eb8bbff
> color sel #60b8bbff
> color sel #5db3b6ff
> color sel #5fb3b6ff
> color sel #5eb2b4ff
> color sel #5eb2b5ff
> color sel #59b2b5ff
> color sel #5cb8bbff
> color sel #4eb8bbff
> color sel #56cccfff
> color sel #4acbcfff
> color sel #4ed7dbff
> color sel #4dd7dbff
> color sel #4ed8dcff
> color sel #4fd8dcff
> color sel #4ed6daff
> color sel #66d7daff
> color sel #60cacdff
> color sel #65cacdff
> color sel #62c3c6ff
> color sel #64c3c6ff
> color sel #60bcbeff
> color sel #62bcbeff
> color sel #5fb6b8ff
[Repeated 1 time(s)]
> color sel #5fb5b8ff
> color sel #5fb6b8ff
> color sel #60b7b9ff
> color sel #60b7baff
> color sel #63bcbfff
> color sel #66c3c6ff
> color sel #68c3c6ff
> color sel #6ac8cbff
> color sel #6dcdd0ff
> color sel #6ecdd0ff
> color sel #70d1d4ff
> color sel #71d2d5ff
> color sel #71d1d5ff
> color sel #69d1d5ff
> color sel #63c6c9ff
> color sel #4fc6c9ff
> color sel #49b8bcff
> color sel #40b8bcff
> color sel #3eb2b6ff
> color sel #35b2b6ff
> color sel #34afb3ff
> color sel #32afb3ff
> color sel #31afb3ff
> color sel #32afb3ff
> color sel #32b0b4ff
> color sel #31b0b4ff
> color sel #32b3b7ff
> color sel #30b3b7ff
> color sel #32bcc0ff
> color sel #2fbcc0ff
> color sel #30c0c4ff
[Repeated 1 time(s)]
> color sel #31c3c8ff
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> color sel #6bc5c8ff
> color sel #519698ff
[Repeated 1 time(s)]
> color sel #52989bff
> color sel #51989bff
> color sel #55a1a3ff
> color sel #54a1a3ff
> color sel #56a5a7ff
> color sel #51a5a7ff
> color sel #55adb0ff
> color sel #41adb0ff
> color sel #44b3b7ff
> color sel #3ab3b7ff
> color sel #37aaadff
> color sel #2aa9adff
> color sel #249296ff
> color sel #1d9296ff
> color sel #1b8487ff
> color sel #198487ff
> color sel #188285ff
> color sel #328518ff
> color sel #2f8518ff
> color sel #208518ff
> color sel #188525ff
> color sel #188537ff
> color sel #188539ff
> color sel #188544ff
> color sel #188575ff
> color sel #187e85ff
> color sel #187385ff
> color sel #186185ff
> color sel #184b85ff
> color sel #183585ff
> color sel #182785ff
> color sel #181e85ff
> color sel #201885ff
> color sel #481885ff
> color sel #601885ff
> color sel #741885ff
> color sel #761885ff
> color sel #811885ff
> color sel #851871ff
> color sel #85185dff
> color sel #85184bff
> color sel #85181fff
> color sel #851818ff
> color sel #85181fff
> color sel #851859ff
> color sel #851868ff
> color sel #851881ff
> color sel #791885ff
> color sel #671885ff
> color sel #431885ff
> color sel #3a1885ff
> color sel #381885ff
> color sel #2d1885ff
> color sel #184285ff
> color sel #186e85ff
> color sel #18855aff
> color sel #188521ff
> color sel #328518ff
> color sel #5c8518ff
> color sel #608518ff
> color sel #768518ff
> color sel #857e18ff
> color sel #857318ff
> color sel #856418ff
> color sel #855918ff
> color sel #854e18ff
> color sel #853318ff
> color sel #851f18ff
> color sel #851818ff
> color sel #851d18ff
> color sel #854518ff
> color sel #855b18ff
> color sel #856818ff
> color sel #857a18ff
> color sel #7b8518ff
> color sel #6b8518ff
> color sel #5e8518ff
> color sel #648529ff
> color sel #66882aff
> color sel #66892aff
> color sel #638921ff
> color sel #668d22ff
> color sel #638d18ff
> color sel #6a981aff
> color sel #679810ff
> color sel #85c415ff
> color sel #84c412ff
> color sel #9fed15ff
> color sel #9eed13ff
> color sel #a7fa14ff
> color sel #a6fa12ff
> color sel #a6fa11ff
> color sel #faf011ff
> color sel #faf411ff
> color sel #edfa11ff
> color sel #d5fa11ff
> color sel #b9fa11ff
> color sel #affa11ff
> color sel #a6fa11ff
> color sel #93fa11ff
> color sel #8efa11ff
> color sel #80fa11ff
> color sel #76fa11ff
> color sel #11fa28ff
> color sel #11fa6aff
> color sel #11fa7dff
> color sel #11faa2ff
> color sel #11fac8ff
> color sel #11faeeff
> color sel #11f3faff
> color sel #11dbfaff
> color sel #11c8faff
> color sel #11b5faff
> color sel #11a2faff
> color sel #1181faff
> color sel #116efaff
> color sel #116afaff
> color sel #1165faff
> color sel #1160faff
> color sel #115cfaff
> color sel #1152faff
> color sel #114dfaff
> color sel #1149faff
> color sel #113ffaff
> color sel #1115faff
> color sel #3911faff
> color sel #4211faff
> color sel #7611faff
> color sel #a111faff
> color sel #a611faff
> color sel #a111faff
> color sel #5111faff
> color sel #1131faff
> color sel #1160faff
> color sel #11c8faff
> color sel #11fae9ff
> color sel #11fab1ff
> color sel #11fa94ff
> color sel #11fa81ff
> color sel #11fa78ff
> color sel #11fa73ff
> color sel #11fa6eff
> color sel #11fa1eff
> color sel #21fa11ff
> color sel #26fa11ff
> color sel #2bfa11ff
> color sel #4cfa11ff
> color sel #63fa11ff
> color sel #89fa11ff
> color sel #a6fa11ff
> color sel #c2fa11ff
> color sel #c7fa11ff
> color sel #cbfa11ff
> color sel #d0fa11ff
> color sel #d5fa11ff
> color sel #defa11ff
> color sel #e4fa40ff
> color sel #c6d938ff
> color sel #c6d937ff
> color sel #c6da37ff
> color sel #c4da26ff
> color sel #cce227ff
> color sel #cbe21fff
> color sel #cfe61fff
> color sel #d0e720ff
> color sel #cfe71fff
> color sel #cfe717ff
> color sel #cee712ff
> color sel #cce512ff
> color sel #c7e011ff
> color sel #c7e010ff
> color sel #bcd40fff
> color sel #bcd40cff
> color sel #aec40bff
> color sel #adc30bff
> color sel #adc30aff
> color sel #adc40aff
> color sel #adc409ff
> color sel #b4cb09ff
> color sel #bcd50aff
> color sel #c4dd0aff
> color sel #c5de0aff
> color sel #c7e00aff
> color sel #cfe90bff
> color sel #d6f10bff
> color sel #dcf80cff
> color sel #e1fd0cff
> color sel #e1fd0bff
> color sel #e2ff0bff
> color sel #e2ff09ff
> color sel #e2ff07ff
> color sel #e1ff05ff
> color sel #e1ff04ff
> color sel #e1ff03ff
> color sel #e0fe03ff
> color sel #e0fe02ff
> color sel #e0fe01ff
> color sel #dffd01ff
> color sel #dffd00ff
> color sel #e0fe00ff
> color sel #fea000ff
> color sel #fea100ff
> color sel #fea300ff
> color sel #fea700ff
> color sel #feb500ff
> color sel #feb700ff
> color sel #fec400ff
> color sel #fecf00ff
> color sel #fed700ff
> color sel #fede00ff
> color sel #fee400ff
> color sel #feea00ff
> color sel #fef500ff
> color sel #fefc00ff
> color sel #fcfe00ff
> color sel #fbfe00ff
> color sel #f9fe00ff
> color sel #f7fe00ff
> color sel #f3fe00ff
> color sel #eefe00ff
> color sel #e6fe00ff
> color sel #e3fe00ff
> color sel #ddfe00ff
> color sel #d4fe00ff
> color sel #d1fe00ff
> color sel #cbfe00ff
> color sel #a7fe00ff
> color sel #9dfe00ff
> color sel #64fe00ff
> color sel #07fe00ff
> color sel #00fe37ff
> color sel #00fe4cff
> color sel #5ffe00ff
> color sel #64fe00ff
> color sel #a7fe00ff
> color sel #acfe00ff
> color sel #bcfe00ff
> color sel #d6fe00ff
> color sel #e0fe00ff
> color sel #e5fe00ff
> color sel #eafe00ff
> color sel #fef800ff
> color sel #fee900ff
> color sel #fee300ff
> color sel #fede00ff
> color sel #fed900ff
> color sel #febf00ff
> color sel #fea000ff
> color sel #fe8c00ff
> color sel #fe9100ff
> color sel #fea000ff
> color sel #feab00ff
> color sel #feba00ff
> color sel #fecf00ff
> color sel #fede00ff
> color sel #fef300ff
> color sel #fefd00ff
> color sel #f5fe00ff
> color sel #f0fe00ff
> color sel #eafe00ff
> color sel #e5fe00ff
> color sel #cbfe00ff
> color sel #c1fe00ff
> color sel #feee00ff
> color sel #fee900ff
> color sel #fed400ff
> color sel #feca00ff
> color sel #fec400ff
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel orange red
> color sel #fed754ff
> color sel #5a4c1eff
> color sel #5a4c1dff
> color sel #5a4b18ff
> color sel #7c6822ff
> color sel #7c661aff
> color sel #af9024ff
> color sel #af8e1eff
> color sel #c6a122ff
> color sel #c6a01eff
> color sel #d2aa20ff
> color sel #d2a818ff
> color sel #e6b71bff
> color sel #e6b71aff
> color sel #eabb1aff
> color sel #ebbb1bff
> color sel #ebbd21ff
> color sel #eec021ff
> color sel #eec129ff
> color sel #f1c42aff
> color sel #f1c52cff
> color sel #f2c52cff
> color sel #f2c630ff
> color sel #f5c831ff
> color sel #f5c934ff
> color sel #f7cb35ff
> color sel #f7cc36ff
> color sel #f7cb36ff
> color sel #f4c936ff
[Repeated 1 time(s)]
> color sel #edc335ff
> color sel #edc332ff
> color sel #e0b72fff
> color sel #e0b72dff
> color sel #dab22cff
> color sel #dab22dff
> color sel #dab32fff
> color sel #dab432ff
> color sel #d8b232ff
[Repeated 1 time(s)]
> color sel #d8b233ff
> color sel #d9b333ff
> color sel #d9b437ff
> color sel #dbb638ff
> color sel #dbb73cff
> color sel #dbb73dff
> color sel #dab73cff
> color sel #d5b23bff
> color sel #cfad39ff
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) #cfcdc8ff
> color (#!1 & sel) #94938fff
> color (#!1 & sel) #949390ff
> color (#!1 & sel) #908f8cff
> color (#!1 & sel) #908e89ff
> color (#!1 & sel) #807f7aff
[Repeated 1 time(s)]
> color (#!1 & sel) #7f7d78ff
> color (#!1 & sel) #807e79ff
> color (#!1 & sel) #8a8882ff
> color (#!1 & sel) #8a8883ff
> color (#!1 & sel) #94928dff
> color (#!1 & sel) #949390ff
> color (#!1 & sel) #a5a4a1ff
> color (#!1 & sel) #a6a5a1ff
> color (#!1 & sel) #a8a7a4ff
> color (#!1 & sel) #a7a6a2ff
> color (#!1 & sel) #a2a19eff
> color (#!1 & sel) #9d9c99ff
> color (#!1 & sel) #989794ff
> color (#!1 & sel) #969592ff
> color (#!1 & sel) #92918eff
> color (#!1 & sel) #91908dff
> color (#!1 & sel) #908f8cff
> color (#!1 & sel) #91908dff
> color (#!1 & sel) #93928fff
> color (#!1 & sel) #999895ff
> color (#!1 & sel) #9b9a97ff
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> color sel cornflower blue
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) #9b947bff
> color (#!1 & sel) #b4ac90ff
> color (#!1 & sel) #b4b0a0ff
> color (#!1 & sel) #a4a092ff
> color (#!1 & sel) #a4a094ff
> color (#!1 & sel) #a09c90ff
> color (#!1 & sel) #a09d94ff
> color (#!1 & sel) #9e9b92ff
> color (#!1 & sel) #9e9c93ff
> color (#!1 & sel) #9e9c94ff
> color (#!1 & sel) #9e9c96ff
> color (#!1 & sel) #9f9d96ff
> color (#!1 & sel) #adaba4ff
> color (#!1 & sel) #c4c1b9ff
> color (#!1 & sel) #c4c1baff
> color (#!1 & sel) #dcdad1ff
> color (#!1 & sel) #dcdbd6ff
> color (#!1 & sel) #d6d5d0ff
> color (#!1 & sel) #d6d5d1ff
> color (#!1 & sel) #cecdc9ff
> color (#!1 & sel) #cececdff
> color (#!1 & sel) #bfbfbfff
[Repeated 1 time(s)]
> color (#!1 & sel) #b9b9b9ff
> color (#!1 & sel) #b3b3b3ff
> color (#!1 & sel) #b1b1b1ff
> color (#!1 & sel) #b0b0b0ff
> color (#!1 & sel) #afafafff
> color (#!1 & sel) #aaaaaaff
> color (#!1 & sel) #aaa9a6ff
> color (#!1 & sel) #9f9e9bff
[Repeated 1 time(s)]
> color (#!1 & sel) #9e9d9aff
[Repeated 1 time(s)]
> color (#!1 & sel) #9d9c9aff
> color (#!1 & sel) #9d9d9bff
> color (#!1 & sel) #959492ff
> color (#!1 & sel) #939291ff
> color (#!1 & sel) #939393ff
> color (#!1 & sel) #8b8b8bff
> color (#!1 & sel) #8d8d8dff
> color (#!1 & sel) #8e8e8dff
[Repeated 1 time(s)]
> color (#!1 & sel) #8f8f8eff
> color sel orange
[Repeated 1 time(s)]
> color sel lime
> color sel forest green
> color sel light gray
> color sel gray
> color sel dark gray
> select clear
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel #8f7a33ff
> color sel #c6a947ff
> color sel #c6ad56ff
> color sel #c8ae57ff
> color sel #c8b267ff
> color sel #c8b36fff
> color sel #c6b26eff
> color sel #c6b475ff
> color sel #c6b680ff
> color sel #c4b47eff
> color sel #c4b688ff
> color sel #bcaf83ff
> color sel #bcb393ff
> color sel #aca386ff
> color sel #aca58dff
> color sel #9e9882ff
> color sel cornflower blue
> color sel medium blue
> color sel blue
> color sel #9e8c4fff
> color sel #4a4225ff
> color sel #524929ff
> color sel #524928ff
> color sel #655931ff
> color sel #65592fff
> color sel #695c30ff
> color sel #305369ff
> color sel #304c69ff
> color sel #304469ff
> color sel #304169ff
> color sel #304069ff
[Repeated 1 time(s)]
> color sel #334470ff
> color sel #344470ff
> color sel #425890ff
> color sel #5672bbff
> color sel #5470bbff
> color sel #5d7dcfff
> color sel #5779cfff
> color sel #5f83e2ff
> color sel #5e83e2ff
> color sel #5f83e3ff
> color sel #5e83e3ff
> color sel #688ae3ff
> color sel #6c90edff
> color sel #7596edff
> color sel #799bf5ff
> color sel #789af3ff
> color sel #7a9bf3ff
> color sel #7696ebff
> color sel #7798ebff
> color sel #6c89d5ff
> color sel #637ec4ff
> color sel #6079bdff
> color sel #607abdff
> color sel #5d76b7ff
> color sel #5f77b7ff
> color sel #5e76b4ff
[Repeated 1 time(s)]
> color sel #6078b7ff
> color sel #7587b7ff
> color sel #7689b8ff
> color sel #7d8eb8ff
> color sel #7e8eb8ff
> color sel #8a9ccaff
> color sel #8196caff
> color sel #8499cfff
> color sel #718bcfff
> color sel #6c85c6ff
> color sel #5877c6ff
> color sel #526eb8ff
> color sel #4565b8ff
> color sel #415fadff
> color sel #3e5cadff
> color sel #3c5aa7ff
> color sel #3b59a7ff
> color sel #3a57a4ff
> color sel #3755a4ff
> color sel #3653a0ff
> color sel #3351a0ff
> color sel #304fa0ff
> color sel #2d4da0ff
> color sel #2e4fa4ff
> color sel #284ba4ff
> color sel #2d53b7ff
> color sel #2a51b7ff
> color sel #2c55c0ff
> color sel #2651c0ff
> color sel #2a59d2ff
> color sel #2656d2ff
> color sel #285be0ff
> color sel #285ce0ff
> color sel #275ae0ff
> color sel #285de7ff
> color sel #275ce7ff
> color sel #285ff0ff
> color sel #2e64f0ff
> color sel #2f66f3ff
> color sel #5883f3ff
> color sel #5a86f9ff
> color sel #759af9ff
> color sel #698ae0ff
> color sel #6c8ce0ff
> color sel #6988d9ff
> color sel #6887d8ff
> color sel #6887d7ff
> color sel #6988d7ff
> color sel #6684d1ff
> color sel #6b87d1ff
> color sel #6581c7ff
> color sel #6681c7ff
> color sel #657fc4ff
> color sel #6580c5ff
> color sel #6680c6ff
> color sel orange red
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG.png width
> 1339 height 936 supersample 3
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG.png width
> 2500 height 1748 supersample 4 transparentBackground true
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG.png width
> 3000 height 2097 supersample 3
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ad7fa8ff
> color sel #729fcfff
> color sel #fce94fff
> color sel #729fcfff
> select clear
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel orange red
> surface ::name="SAM" resolution 2
2 Gaussian surfaces, threshold level 1.970 - 1.971
> surface ::name="SAM" resolution 2.2
2 Gaussian surfaces, threshold level 1.497 - 1.509
> surface ::name="SAM" resolution 2.3
2 Gaussian surfaces, threshold level 1.307 - 1.332
> select #1/A :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> color sel blue
> color sel yellow
> color sel cornflower blue
> color sel medium blue
> color sel purple
> color sel hot pink
> color sel gray
> color sel black
> color sel red
> color sel orange red
> color sel orange
> color sel yellow
> color sel lime
> color sel #bf404fff
> color sel #80a1c4ff
> color sel #a5c0f1ff
> color sel #f4b6b6ff
> color sel #fba47bff
> color sel #bf2121ff
> color sel #a41c1cff
> color sel #a41d1dff
> color sel #a61d1dff
> color sel #a61f1fff
> color sel #b12222ff
> color sel #b12424ff
> color sel #c52828ff
> color sel #c72828ff
> color sel #c82929ff
> color sel #c92929ff
> color sel #c91f1fff
> color sel #da2222ff
> color sel #ccda22ff
> color sel #c8da22ff
> color sel #7dda22ff
> color sel #22da37ff
> color sel #22da68ff
> color sel #22daacff
> color sel #22d5daff
> color sel #22a8daff
> color sel #227bdaff
> color sel #225ddaff
> color sel #224adaff
> color sel #2243daff
> color sel #223fdaff
> color sel #223bdaff
> color sel #2237daff
> color sel #222cdaff
> color sel #2b22daff
> color sel #3a22daff
> color sel #4922daff
> color sel #5022daff
> color sel #6b22daff
> color sel #7a22daff
> color sel #3a22daff
> color sel #3222daff
> color sel #223fdaff
> color sel #2246daff
> color sel #1b41daff
> color sel #1a3fd5ff
[Repeated 1 time(s)]
> color sel #163bd5ff
> color sel #1539caff
> color sel #0b31caff
> color sel #0a2bb1ff
> color sel #0829b1ff
> color sel #0725a2ff
> color sel #0826a2ff
> color sel #072392ff
> color sel #0a2592ff
> color sel #092285ff
> color sel #0a2285ff
> color sel #0a2180ff
> color sel #0a217fff
> color sel #091f76ff
> color sel #081e76ff
> color sel #081d73ff
> color sel #081c70ff
> color sel #071c70ff
> color sel #071c6fff
> select #1/A :85-129 :354-397
733 atoms, 746 bonds, 89 residues, 1 model selected
> color sel #061b6fff
> color sel #061c76ff
> color sel #061c74ff
> color sel #061a6fff
> color sel #061969ff
[Repeated 1 time(s)]
> color sel #061968ff
[Repeated 1 time(s)]
> color sel #061967ff
> color sel #061968ff
[Repeated 1 time(s)]
> color sel #071a68ff
> color sel #071a69ff
[Repeated 1 time(s)]
> color sel #071b6aff
> color sel #081b6aff
> color sel #081c6cff
> color sel #091c6cff
> color sel #091c6dff
[Repeated 3 time(s)]
> select clear
> select #1/B :85-129 :354-397
729 atoms, 742 bonds, 89 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel black
> select clear
> select #1/B :85-129 :354-397
729 atoms, 742 bonds, 89 residues, 1 model selected
> ui tool show "Color Actions"
> color sel black
> color sel #2e3436ff
> select clear
> color #2e3436ff
[Repeated 1 time(s)]
> undo
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel cornflower blue
> color sel dark gray
Drag select of 2 residues
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel cornflower blue
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color sel dark gray
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel #a5c0f1ff
> color sel #091c6dff
> color sel #4087bfff
> color sel #458abfff
> color sel #4a94ceff
> color sel #5097ceff
> color sel #539cd5ff
> color sel #67a5d5ff
> color sel #6caee0ff
> color sel #76b2e0ff
> color sel #79b6e6ff
> color sel #7bb7e6ff
> color sel #7ebbebff
> color sel #81bcebff
> color sel #84c1f0ff
> color sel #85c1f0ff
> color sel #85c2f1ff
> color sel #86c2f1ff
> color sel #86c3f1ff
> color sel #87c3f1ff
> color sel #8fc6f1ff
> color sel #87bbe3ff
> color sel #75a1c4ff
> color sel #76a2c4ff
> color sel #739ebfff
> color sel #79a1bfff
> color sel #7297b4ff
> color sel #7398b5ff
> color sel #7ba3c2ff
> color sel #80aacaff
> color sel #81aacaff
> color sel #89b4d6ff
> color sel #8bb5d6ff
> color sel #8eb9dbff
> color sel #8fbadbff
> color sel #8db8daff
> color sel #8fb9daff
> color sel #86adccff
> color sel #85accaff
> color sel #84accaff
> color sel #8ab3d3ff
> color sel #85b1d3ff
> color sel #8cbadeff
> color sel #8dbbe0ff
> color sel #8bbae0ff
> color sel #90c1e8ff
> color sel #8ec0e8ff
> color sel #92c7f0ff
> color sel #91c6f0ff
> color sel #91c6efff
> color sel #90c5efff
> color sel #90c5eeff
> color sel #8fc4eeff
> color sel #8ec4edff
> color sel #8dc3edff
> color sel #8dc3ecff
> color sel #8cc2ecff
> color sel #8cc2ebff
> color sel #8bc1ebff
> select clear
> color #8bc1ebff
[Repeated 1 time(s)]
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color sel dark gray
> select clear
> select #1/A :85-129 :354-397
733 atoms, 746 bonds, 89 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #204a87ff
> color sel #409abfff
> color sel #4094bfff
> color sel #4087bfff
> color sel #407dbfff
> color sel #406ebfff
> color sel #405bbfff
> color sel #4054bfff
> color sel #4051bfff
> color sel #4054bfff
> color sel #4068bfff
> color sel #4085bfff
> color sel #4087bfff
> color sel #2f80bfff
> color sel #3185c6ff
> color sel #3085c6ff
> color sel #3084c5ff
> color sel #2780c5ff
> color sel #2477b8ff
> color sel #1f75b8ff
> color sel #1e70afff
> color sel #176dafff
> color sel #1665a2ff
> color sel #1163a2ff
> color sel #105d98ff
> color sel #0d5b98ff
> color sel #0c5893ff
> color sel #0b5893ff
> color sel #0b5791ff
> color sel #0a5691ff
[Repeated 1 time(s)]
> color sel #045391ff
> color sel #045492ff
> color sel #035492ff
> color sel #036e92ff
> color sel #037192ff
> color sel #037792ff
> color sel #037f92ff
> color sel #037c92ff
> color sel #037b92ff
> color sel #037392ff
> color sel #036f92ff
> color sel #036e92ff
[Repeated 1 time(s)]
> color sel #036d92ff
> color sel #0a6f92ff
> color sel #085a77ff
> color sel #085c77ff
[Repeated 1 time(s)]
> color sel #075c76ff
> color sel #0c5d76ff
> color sel #0b536aff
> color sel #0f546aff
> color sel #0e5166ff
> color sel #0f5166ff
[Repeated 1 time(s)]
> color sel #0f5267ff
> color sel #105267ff
> color sel #105368ff
[Repeated 1 time(s)]
> color sel #105369ff
> color sel #0f5369ff
> color sel #0f546aff
> color sel #0a536aff
> color sel #0a5871ff
> color sel #055771ff
> color sel #065e7aff
> color sel #061f7aff
> color sel #06217aff
> color sel #062b7aff
> color sel #06427aff
> color sel #064e7aff
> color sel #06557aff
> color sel #065a7aff
> color sel #06687aff
> color sel #06747aff
> color sel #06767aff
> color sel #06717aff
> color sel #06577aff
> color sel #06427aff
[Repeated 2 time(s)]
> select clear
> select #1/B :85-129 :354-397
729 atoms, 742 bonds, 89 residues, 1 model selected
> color sel dim gray
> color sel #555753ff
[Repeated 2 time(s)]
> select clear
> surface ::name="SAM" resolution 2.3
2 Gaussian surfaces, threshold level 1.307 - 1.332
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel orange red
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> color sel purple
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG.png width
> 3000 height 2097 supersample 4 transparentBackground true
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
Drag select of fuzja.pdb_B Gaussian surface, 8880 of 17788 triangles
[Repeated 1 time(s)]
> hide surfaces
> hide cartoons
> show cartoons
> hide atoms
> hide cartoons
[Repeated 1 time(s)]
> show cartoons
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
Drag select of fuzja.pdb_B Gaussian surface, 5398 of 17788 triangles
Drag select of fuzja.pdb_B Gaussian surface, 2240 of 17788 triangles
> surface ::name="SAM" resolution 2.3
2 Gaussian surfaces, threshold level 1.307 - 1.332
> surface ::name="SAM" resolution 2
2 Gaussian surfaces, threshold level 1.970 - 1.971
> surface ::name="SAM" resolution 0
> surface ::name="SAM" resolution 1
2 Gaussian surfaces, threshold level 15.582 - 15.613
> surface ::name="SAM" resolution 0.1
Unable to allocate 48.5 GiB for an array with shape (3198, 1320, 3086) and
data type float32
> show cartoons
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> surface ::name="SAM" resolution 2.3
2 Gaussian surfaces, threshold level 1.307 - 1.332
> surface ::name="SAM" resolution 2.2
2 Gaussian surfaces, threshold level 1.497 - 1.509
> surface ::name="SAM" resolution 2.1
2 Gaussian surfaces, threshold level 1.707
> surface ::name="SAM" resolution 2.2
2 Gaussian surfaces, threshold level 1.497 - 1.509
> hide atoms
> show atoms
> hide atoms
> show atoms
> hide atoms
> select clear
> hide cartoons
> hide atoms
> hide cartoons
> hide surfaces
[Repeated 4 time(s)]
> hide cartoons
> hide atoms
> open /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/fuzja.pdb
Summary of feedback from opening /home/users/fbruno/Postdoc/Projeto-TrmD-
Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/fuzja.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-06-02 Time 15:26:10 CEST +0200 (1654176370.09 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/ania_k/Phenix_output/resolutions-
diff/195A/fuzja_1_18_I.mtz
45 messages similar to the above omitted
Chain information for fuzja.pdb #2
---
Chain | Description
A | No description available
B | No description available
> surface ::name="SAM" resolution 0.1
Unable to allocate 140. GiB for an array with shape (2452, 2624, 5834) and
data type float32
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!1 cartoons
> show #!2 models
> hide #!1 models
> show #!1 models
> select #/A
Expected an objects specifier or a keyword
> select /A
7064 atoms, 7218 bonds, 874 residues, 2 models selected
> select #2
7589 atoms, 7000 bonds, 2 pseudobonds, 1583 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select ::name="SAM"
216 atoms, 232 bonds, 8 residues, 2 models selected
> show sel atoms
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #1/B:601@CB
1 atom, 1 residue, 1 model selected
Drag select of 3 residues
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/A SAM
Expected a keyword
> select #1/A ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> select #1/B ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #1/A ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> style sel ball
Changed 54 atom styles
> color sel byhetero
> color sel gray
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1344, in <lambda>
cmd="color %%s %s" % spaced_name: run(cmd))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1504, in _run_surf_command
run(self.session, cmd % selector)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
> color sel byhetero
> select clear
> select #1/A ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> color sel orange
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1344, in <lambda>
cmd="color %%s %s" % spaced_name: run(cmd))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1504, in _run_surf_command
run(self.session, cmd % selector)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
> ui tool show "Color Actions"
> color sel #bf8140ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
> color sel #bf8340ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MSI
Model: MS-7A70
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 5.7Gi 22Gi 206Mi 2.8Gi 25Gi
Swap: 7.6Gi 0B 7.6Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)
Subsystem: PNY GP104 [GeForce GTX 1070] [196e:119d]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.0.6
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (3)
comment:1 by , 3 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Coloring surface: self.vertices is None |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
This error in color command was caused by the previous failed surface calculation which left an invalid surface with vertices = None.
> surface ::name="SAM" resolution 0.1 Unable to allocate 140. GiB for an array with shape (2452, 2624, 5834) and data type float32
I made the code create a surface with 0 vertices so it will not cause subsequent errors.
comment:3 by , 3 years ago
This error came about because you tried to compute a gaussian surface with resolution 0.1 Angstroms and that takes too much memory since it tries to make a 0.1 Anstrom grid covering your entire molecule. It is not sensible to try to compute a 0.1 Angstrom Gaussian surface. This would make each atom a tiny point about 0.1 Angstrom in radius so you would just get a surface of many scattered tiny spheres at the atom centers.
To correct this problem in your current ChimeraX you can close the failed surface, for instance if the failed surface is model #1.1, use "close #1.1". Or you can recompute the surface with a resolution where it does not fail "surface ::name="SAM" resolution 2"
Molecular surfaces are usually solvent excluded surfaces which use the radii of the individual atoms and do not specify a resolution. If you specify a resolution it gives a Gaussian surface which is usually only useful for low resolutions (e.g. larger than 3 Angstroms). Read the ChimeraX surface command documentation to understand the differences better.
Note:
See TracTickets
for help on using tickets.
Reported by Fernando Bruno da Silva