Nucleotides ladder: subtracting Nones

[lochuynh@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

Log from Thu May 28 14:57:35 2020UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3Q1R format mmCIF fromDatabase pdb

Summary of feedback from opening 3Q1R fetched from pdb  
---  
notes | Fetching compressed mmCIF 3q1r from
http://files.rcsb.org/download/3q1r.cif  
  
  
  
  
| Summary of feedback from opening
/Users/LocHuynh/Downloads/ChimeraX/PDB/3q1r.cif  
  
---  
  
  
  
  
note | Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
  
  
  
  
3q1r title:  
Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and
in the presence of 5' leader [more info...]  
  
Chain information for 3q1r #1  
---  
Chain | Description  
A | Ribonuclease P protein component  
B | RNase P RNA  
C | TRNA (phe)  
D | TRNA 5' leader  
  
Non-standard residues in 3q1r #1  
---  
MG — magnesium ion  
  
  

> set bgColor black

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #1/B

Alignment identifier is 1.B  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1.A  
Alignment identifier is 1.A  

> show sel cartoons

> sequence chain #1/C

Alignment identifier is 1.C  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected  

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> show sel atoms

> hide sel atoms

> hide sel cartoons

> select /A:6-117

973 atoms, 989 bonds, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> hide sel atoms

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 65 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 65 atom styles  

> show sel cartoons

> show sel atoms

> color sel bynucleotide

> nucleotides sel atoms

> style nucleic & sel stick

Changed 109 atom styles  

> color sel bynucleotide

> color sel byhetero

> color sel bychain

> color sel byhetero

> hide sel cartoons

> select :MG

5 atoms, 1 model selected  

> color red

> color sel red

> color sel green

> color sel lime

> color sel lime green

Unknown command: color-spec  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel pink

> color sel deep pink

> color sel magenta

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> color sel bychain

> color sel bychain

> color sel green

> color sel dark green

> color sel sea green

> color sel medium sea green

> color sel sea green

> color sel teal

> color sel dark cyan

> color sel byhetero

> select up

7384 atoms, 8253 bonds, 1 model selected  

> select down

7380 atoms, 8253 bonds, 1 model selected  

> select /B:50@C4'

1 atom, 1 model selected  

> select /B:51@C5

1 atom, 1 model selected  

> select up

65 atoms, 72 bonds, 1 model selected  

> color sel lemonchiffon

> color sel byhetero

> color sel khaki

> color sel wheat

> color sel tan

> color sel byhetero

> color sel teal

> color sel byhetero

> color sel slate blue

> color sel byhetero

> color sel dark slate blue

> color sel byhetero

> color sel bynucleotide

> color sel dark slate blue

> color sel bynucleotide

> color sel byhetero

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> color sel byhetero

> color sel dark slate blue

> color sel byhetero

> set bgColor white

> select :MG

5 atoms, 1 model selected  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel lime green

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> style sel stick

Changed 24 atom styles  

> style sel sphere

Changed 24 atom styles  

> style sel stick

Changed 24 atom styles  

> style sel ball

Changed 24 atom styles  

> style sel stick

Changed 24 atom styles  

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> show sel cartoons

> color sel slate blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel midnight blue

> color sel red

> show sel atoms

> show sel atoms

> style sel stick

Changed 40 atom styles  

> hide sel cartoons

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> show sel surfaces

> style sel stick

Changed 40 atom styles  

> hide sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> show sel atoms

> show sel atoms

> color sel byhetero

> style sel stick

Changed 40 atom styles  

> hide sel cartoons

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1.A  
Alignment identifier is 1.A  

> mlp sel

mlp: no amino acids specified  

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> show sel atoms

> hide sel cartoons

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> style sel sphere

Changed 973 atom styles  

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> color sel byhetero

> color sel bychain

> color sel tan

> color sel brown

> color sel chocolate

> color sel burly wood

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel beige

> color sel tan

> select sequence CCCUCGG

146 atoms, 161 bonds, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 146 atom styles  

> show sel atoms

> hide sel atoms

> nucleotides sel slab

> style nucleic & sel stick

Changed 7380 atom styles  

> nucleotides sel ladder

> show sel atoms

> set bgColor black

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected  

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected  

> select /A:6-117

973 atoms, 989 bonds, 1 model selected  

> sequence chain #1/D

Alignment identifier is 1.D  

> sequence chain #1/C

Alignment identifier is 1.C  

> sequence chain #1/B

Destroying pre-existing alignment with identifier 1.B  
Alignment identifier is 1.B  

> select sequence AGCGUCGG

174 atoms, 194 bonds, 1 model selected  

> select sequence GGGGGG

138 atoms, 155 bonds, 1 model selected  

> select sequence GGGGGGAA

182 atoms, 205 bonds, 1 model selected  

> select sequence GGGGGGAA

182 atoms, 205 bonds, 1 model selected  

> nucleotides sel ladder

> nucleotides sel fill

> style nucleic & sel stick

Changed 182 atom styles  

> select sequence GGGGGGAAACUUCC

304 atoms, 340 bonds, 15 pseudobonds, 2 models selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 304 atom styles  

> select clear

> select sequence ggagc

333 atoms, 372 bonds, 1 model selected  

> select sequence ggagcg

134 atoms, 150 bonds, 1 model selected  

> select sequence ggagcg

134 atoms, 150 bonds, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 237 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 237 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 237 atom styles  

> select clear

> select /B:249

20 atoms, 21 bonds, 1 model selected  

> select /B:248

20 atoms, 21 bonds, 1 model selected  

> style sel sphere

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> mlp sel

mlp: no amino acids specified  

> style sel sphere

Changed 40 atom styles  

> style sel sphere

Changed 40 atom styles  

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting flat

> lighting flat

> graphics silhouettes false

> lighting soft

> set bgColor white

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> style sel sphere

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> hide sel atoms

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 40 atom styles  

> style sel ball

Changed 40 atom styles  

> set bgColor black

> style sel sphere

Changed 40 atom styles  

> sequence chain #1/A

Alignment identifier is 1.A  

> color sel bychain

> color sel byhetero

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> color sel bynucleotide

> rainbow sel

> color bfactor sel

973 atoms, 112 residues, 1 surfaces, atom bfactor range 80 to 80  

> color sel byhetero

> color sel bychain

> color sel tan

> show sel surfaces

> style sel stick

Changed 40 atom styles  

> color sel red

> color sel byhetero

Unknown command: tan  

> color sel byhetero

> color sel tan

> color sel byhetero

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel purple

> color sel byhetero

> lighting simple

> lighting simple

> lighting soft

> lighting simple

> hide sel surfaces

> style sel sphere

Changed 40 atom styles  

> select /B:51

23 atoms, 25 bonds, 1 model selected  

> hide sel cartoons

> color sel blue

> color sel navy

> color sel byhetero

> select /B:52

20 atoms, 21 bonds, 1 model selected  

> hide sel cartoons

> show sel cartoons

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> color sel navy

> color sel byhetero

> lighting soft

> lighting simple

> select /C:1@C3'

1 atom, 1 model selected  

> select up

24 atoms, 26 bonds, 1 model selected  

> select /C:1@P

1 atom, 1 model selected  

> select up

24 atoms, 26 bonds, 1 model selected  

> select /B:52

20 atoms, 21 bonds, 1 model selected  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

23 atoms, 25 bonds, 1 model selected  

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild  
_rebuild_molecule('internal', mol)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1191, in make_ladder  
midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1])  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
Error processing trigger "new frame":  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1191, in make_ladder  
midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.19
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Eric Pettersen]

Reported by Loc Huynh

[Greg Couch]

Please update your version of ChimeraX to fix this bug. The only reason to stick with version 0.93 is if you are using the ISOLDE plugin. And a new version of that should be available within a week or two.