Coloring surface: self.vertices is None

[f.bruno@…]

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.  
  

> color sel #bf741fff

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 #b06b1dff

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 #b06c1dff

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 #b06d1dff

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 #b46f1eff

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 #b47223ff

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 #c47c27ff

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 #c47d29ff

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 #cf832bff

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 #cf842dff

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 #d1862dff

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 #d1862fff

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 #d2872fff

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 #d4882fff

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 #d48830ff

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 #d68a31ff

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 #d78b31ff

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       203Mi       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

[pett]

Duplicate of #7466