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#2807 closed defect (fixed)

'NoneType' object has no attribute 'needs_update' after 2D labels closed

Reported by:	shiran.dror@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-12-23)
Description
Changed preset to "Interactive" got this error, then changed background to white and got it again

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/bukau_lab/research proposal/ribosome_structure/chimerax/4U3U.cxc"

> open 4U3U

4u3u title:  
Crystal structure of Cycloheximide bound to the yeast 80S ribosome [more
info...]  
  
Chain information for 4u3u #1  
---  
Chain | Description  
1 5 | 25S ribosomal RNA  
2 6 | 18S ribosomal RNA  
3 7 | 5S ribosomal RNA  
4 8 | 5.8S ribosomal RNA  
C0 c0 | 40S ribosomal protein S10-A  
C1 c1 | 40S ribosomal protein S11-A  
C2 c2 | 40S ribosomal protein S12  
C3 c3 | 40S ribosomal protein S13  
C4 c4 | 40S ribosomal protein S14-A  
C5 c5 | 40S ribosomal protein S15  
C6 c6 | 40S ribosomal protein S16-A  
C7 c7 | 40S ribosomal protein S17-A  
C8 c8 | 40S ribosomal protein S18-A  
C9 c9 | 40S ribosomal protein S19-A  
D0 d0 | 40S ribosomal protein S20  
D1 d1 | 40S ribosomal protein S21-A  
D2 d2 | 40S ribosomal protein S22-A  
D3 d3 | 40S ribosomal protein S23-A  
D4 d4 | 40S ribosomal protein S24-A  
D5 d5 | 40S ribosomal protein S25-A  
D6 d6 | 40S ribosomal protein S26-B  
D7 d7 | 40S ribosomal protein S27-A  
D8 d8 | 40S ribosomal protein S28-A  
D9 d9 | 40S ribosomal protein S29-A  
E0 | 40S ribosomal protein S30-A  
E1 | Ubiquitin-40S ribosomal protein S31  
L2 l2 | 60S ribosomal protein L2-A  
L3 l3 | 60S ribosomal protein L3  
L4 l4 | 60S ribosomal protein L4-A  
L5 l5 | 60S ribosomal protein L5  
L6 l6 | 60S ribosomal protein L6-A  
L7 l7 | 60S ribosomal protein L7-A  
L8 l8 | 60S ribosomal protein L8-A  
L9 l9 | 60S ribosomal protein L9-A  
M0 m0 | 60S ribosomal protein L10  
M1 m1 | 60S ribosomal protein L11-B  
M3 m3 | 60S ribosomal protein L13-A  
M4 m4 | 60S ribosomal protein L14-A  
M5 m5 | 60S ribosomal protein L15-A  
M6 m6 | 60S ribosomal protein L16-A  
M7 m7 | 60S ribosomal protein L17-A  
M8 m8 | 60S ribosomal protein L18-A  
M9 m9 | 60S ribosomal protein L19-A  
N0 n0 | 60S ribosomal protein L20-A  
N1 n1 | 60S ribosomal protein L21-A  
N2 n2 | 60S ribosomal protein L22-A  
N3 n3 | 60S ribosomal protein L23-A  
N4 n4 | 60S ribosomal protein L24-A  
N5 n5 | 60S ribosomal protein L25  
N6 n6 | 60S ribosomal protein L26-A  
N7 n7 | 60S ribosomal protein L27-A  
N8 n8 | 60S ribosomal protein L28  
N9 n9 | 60S ribosomal protein L29  
O0 o0 | 60S ribosomal protein L30  
O1 o1 | 60S ribosomal protein L31-A  
O2 o2 | 60S ribosomal protein L32  
O3 o3 | 60S ribosomal protein L33-A  
O4 o4 | 60S ribosomal protein L34-A  
O5 o5 | 60S ribosomal protein L35-A  
O6 o6 | 60S ribosomal protein L36-A  
O7 o7 | 60S ribosomal protein L37-A  
O8 o8 | 60S ribosomal protein L38  
O9 o9 | 60S ribosomal protein L39  
Q0 q0 | Ubiquitin-60S ribosomal protein L40  
Q1 q1 | 60S ribosomal protein L41-A  
Q2 q2 | 60S ribosomal protein L42-A  
Q3 q3 | 60S ribosomal protein L43-A  
S0 s0 | 40S ribosomal protein S0-A  
S1 s1 | 40S ribosomal protein S1-A  
S2 s2 | 40S ribosomal protein S2  
S3 s3 | 40S ribosomal protein S3  
S4 s4 | 40S ribosomal protein S4-A  
S5 s5 | 40S ribosomal protein S5  
S6 s6 | 40S ribosomal protein S6-A  
S7 s7 | 40S ribosomal protein S7-A  
S8 s8 | 40S ribosomal protein S8-A  
S9 s9 | 40S ribosomal protein S9-A  
SM sM | Suppressor protein STM1  
SR sR | Guanine nucleotide-binding protein subunit beta-like protein  
e0 | 40S ribosomal protein S30-A  
e1 | Ubiquitin-40S ribosomal protein S31  
m2 | UNKNOWN PROTEIN m2  
p0 | 60S acidic ribosomal protein P0  
p1 | UNKNOWN PROTEIN p1  
p2 | UNKNOWN PROTEIN p2  
  
Non-standard residues in 4u3u #1  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
MG — magnesium ion  
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)  
ZN — zinc ion  
  
4u3u mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
  

> hide atoms

> hide ribbons

> show surfaces

> color gray

> select protein

179694 atoms, 182766 bonds, 15 pseudobonds, 2 models selected  

> color sel white

> select /L0-Q9

49865 atoms, 50591 bonds, 129 pseudobonds, 3 models selected  

> color sel #aaffff

> select /C0-D9,S0-S9

34555 atoms, 35067 bonds, 51 pseudobonds, 3 models selected  

> color sel #fad0ff

> select protein sequence .{1}$

904 atoms, 809 bonds, 1 model selected  

> color sel red

> show sel atoms

> select protein sequence w(b)

264 atoms, 276 bonds, 1 model selected  

> color sel green

> show sel atoms

> hide /c0-s9 surfaces

> hide /c0-s9 atoms

> hide /5-9 surfaces

> hide /5-9 atoms

> hide /sM,sR surfaces

> hide /sM,sR atoms

> ~select

Nothing selected  

> view

executed 4U3U.cxc  

> set bgColor white

> close session

> open "C:\bukau_lab\research proposal\ribosome_structure\chimerax\4U3U.cxc"

> open 4U3U

4u3u title:  
Crystal structure of Cycloheximide bound to the yeast 80S ribosome [more
info...]  
  
Chain information for 4u3u #1  
---  
Chain | Description  
1 5 | 25S ribosomal RNA  
2 6 | 18S ribosomal RNA  
3 7 | 5S ribosomal RNA  
4 8 | 5.8S ribosomal RNA  
C0 c0 | 40S ribosomal protein S10-A  
C1 c1 | 40S ribosomal protein S11-A  
C2 c2 | 40S ribosomal protein S12  
C3 c3 | 40S ribosomal protein S13  
C4 c4 | 40S ribosomal protein S14-A  
C5 c5 | 40S ribosomal protein S15  
C6 c6 | 40S ribosomal protein S16-A  
C7 c7 | 40S ribosomal protein S17-A  
C8 c8 | 40S ribosomal protein S18-A  
C9 c9 | 40S ribosomal protein S19-A  
D0 d0 | 40S ribosomal protein S20  
D1 d1 | 40S ribosomal protein S21-A  
D2 d2 | 40S ribosomal protein S22-A  
D3 d3 | 40S ribosomal protein S23-A  
D4 d4 | 40S ribosomal protein S24-A  
D5 d5 | 40S ribosomal protein S25-A  
D6 d6 | 40S ribosomal protein S26-B  
D7 d7 | 40S ribosomal protein S27-A  
D8 d8 | 40S ribosomal protein S28-A  
D9 d9 | 40S ribosomal protein S29-A  
E0 | 40S ribosomal protein S30-A  
E1 | Ubiquitin-40S ribosomal protein S31  
L2 l2 | 60S ribosomal protein L2-A  
L3 l3 | 60S ribosomal protein L3  
L4 l4 | 60S ribosomal protein L4-A  
L5 l5 | 60S ribosomal protein L5  
L6 l6 | 60S ribosomal protein L6-A  
L7 l7 | 60S ribosomal protein L7-A  
L8 l8 | 60S ribosomal protein L8-A  
L9 l9 | 60S ribosomal protein L9-A  
M0 m0 | 60S ribosomal protein L10  
M1 m1 | 60S ribosomal protein L11-B  
M3 m3 | 60S ribosomal protein L13-A  
M4 m4 | 60S ribosomal protein L14-A  
M5 m5 | 60S ribosomal protein L15-A  
M6 m6 | 60S ribosomal protein L16-A  
M7 m7 | 60S ribosomal protein L17-A  
M8 m8 | 60S ribosomal protein L18-A  
M9 m9 | 60S ribosomal protein L19-A  
N0 n0 | 60S ribosomal protein L20-A  
N1 n1 | 60S ribosomal protein L21-A  
N2 n2 | 60S ribosomal protein L22-A  
N3 n3 | 60S ribosomal protein L23-A  
N4 n4 | 60S ribosomal protein L24-A  
N5 n5 | 60S ribosomal protein L25  
N6 n6 | 60S ribosomal protein L26-A  
N7 n7 | 60S ribosomal protein L27-A  
N8 n8 | 60S ribosomal protein L28  
N9 n9 | 60S ribosomal protein L29  
O0 o0 | 60S ribosomal protein L30  
O1 o1 | 60S ribosomal protein L31-A  
O2 o2 | 60S ribosomal protein L32  
O3 o3 | 60S ribosomal protein L33-A  
O4 o4 | 60S ribosomal protein L34-A  
O5 o5 | 60S ribosomal protein L35-A  
O6 o6 | 60S ribosomal protein L36-A  
O7 o7 | 60S ribosomal protein L37-A  
O8 o8 | 60S ribosomal protein L38  
O9 o9 | 60S ribosomal protein L39  
Q0 q0 | Ubiquitin-60S ribosomal protein L40  
Q1 q1 | 60S ribosomal protein L41-A  
Q2 q2 | 60S ribosomal protein L42-A  
Q3 q3 | 60S ribosomal protein L43-A  
S0 s0 | 40S ribosomal protein S0-A  
S1 s1 | 40S ribosomal protein S1-A  
S2 s2 | 40S ribosomal protein S2  
S3 s3 | 40S ribosomal protein S3  
S4 s4 | 40S ribosomal protein S4-A  
S5 s5 | 40S ribosomal protein S5  
S6 s6 | 40S ribosomal protein S6-A  
S7 s7 | 40S ribosomal protein S7-A  
S8 s8 | 40S ribosomal protein S8-A  
S9 s9 | 40S ribosomal protein S9-A  
SM sM | Suppressor protein STM1  
SR sR | Guanine nucleotide-binding protein subunit beta-like protein  
e0 | 40S ribosomal protein S30-A  
e1 | Ubiquitin-40S ribosomal protein S31  
m2 | UNKNOWN PROTEIN m2  
p0 | 60S acidic ribosomal protein P0  
p1 | UNKNOWN PROTEIN p1  
p2 | UNKNOWN PROTEIN p2  
  
Non-standard residues in 4u3u #1  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
MG — magnesium ion  
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)  
ZN — zinc ion  
  
4u3u mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
  

> hide atoms

> hide ribbons

> show surfaces

> color gray

> select protein

179694 atoms, 182766 bonds, 15 pseudobonds, 2 models selected  

> color sel white

> select /L0-Q9

49865 atoms, 50591 bonds, 129 pseudobonds, 3 models selected  

> color sel #aaffff

> select /C0-D9,S0-S9

34555 atoms, 35067 bonds, 51 pseudobonds, 3 models selected  

> color sel #fad0ff

> select protein sequence .{1}$

904 atoms, 809 bonds, 1 model selected  

> color sel red

> show sel atoms

> select protein sequence w(b)

264 atoms, 276 bonds, 1 model selected  

> color sel green

> show sel atoms

> hide /c0-s9 surfaces

> hide /c0-s9 atoms

> hide /5-9 surfaces

> hide /5-9 atoms

> hide /sM,sR surfaces

> hide /sM,sR atoms

> ~select

Nothing selected  

> view

executed 4U3U.cxc  

> select /E1

567 atoms, 577 bonds, 4 pseudobonds, 2 models selected  

> select clear

> close session

> open "C:\bukau_lab\research proposal\ribosome_structure\chimerax\ribosome
> model (PDB 6T4Q).cxs" format session

opened ChimeraX session  

> view

> lighting full

> save C:\Users\Shiran\Desktop\image1.png supersample 3

> save C:\Users\Shiran\Desktop\image1.png supersample 5

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  

> save C:\Users\Shiran\Desktop\ribosomal_proteins_c_terminal.png supersample 5

> save C:\Users\Shiran\Desktop\ribosomal_proteins_c_terminal_2.png supersample
> 5

> close session

> open "C:/bukau_lab/research proposal/ribosome_structure/chimerax/6T4Q.cxc"

> open 6T4Q

6t4q title:  
Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon
combination. [more info...]  
  
Chain information for 6t4q #1  
---  
Chain | Description  
5 | mRNA  
6 | ICG tRNA Arg (P/P)  
7 | tRNA (E/E)  
8 | nascent chain  
C1 | 25S rRNA  
C2 | 18S rRNA  
C3 | 5.8S rRNA  
C4 | 5S rRNA  
LA | 60S ribosomal protein L2-A  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4-A  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6-B  
LF | 60S ribosomal protein L7-A  
LG | 60S ribosomal protein L8-A  
LH | 60S ribosomal protein L9-A  
LI | 60S ribosomal protein L10  
LJ | 60S ribosomal protein L11-B  
LL | 60S ribosomal protein L13-A  
LM | 60S ribosomal protein L14-A  
LN | 60S ribosomal protein L15-A  
LO | 60S ribosomal protein L16-A  
LP | 60S ribosomal protein L17-A  
LQ | 60S ribosomal protein L18-A  
LR | 60S ribosomal protein L19-A  
LS | 60S ribosomal protein L20-A  
LT | 60S ribosomal protein L21-A  
LU | 60S ribosomal protein L22-A  
LV | 60S ribosomal protein L23-A  
LW | 60S ribosomal protein L24-A  
LX | 60S ribosomal protein L25  
LY | 60S ribosomal protein L26-A  
LZ | 60S ribosomal protein L27-A  
La | 60S ribosomal protein L28  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31-A  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L33-A  
Lg | 60S ribosomal protein L34-A  
Lh | 60S ribosomal protein L35-A  
Li | 60S ribosomal protein L36-A  
Lj | 60S ribosomal protein L37-A  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41-A  
Lo | 60S ribosomal protein L42-A  
Lp | 60S ribosomal protein L43-A  
SA | 40S ribosomal protein S0-A  
SB | 40S ribosomal protein S1-A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4-A  
SF | Rps5p  
SG | 40S ribosomal protein S6-A  
SH | 40S ribosomal protein S7-A  
SI | 40S ribosomal protein S8-A  
SJ | 40S ribosomal protein S9-A  
SK | 40S ribosomal protein S10-A  
SL | 40S ribosomal protein S11-A  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14-B  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16-A  
SR | 40S ribosomal protein S17-A  
SS | 40S ribosomal protein S18-A  
ST | 40S ribosomal protein S19-A  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21-A  
SW | 40S ribosomal protein S22-A  
SX | 40S ribosomal protein S23-A  
SY | 40S ribosomal protein S24-A  
SZ | 40S ribosomal protein S25-A  
Sa | 40S ribosomal protein S26-B  
Sb | 40S ribosomal protein S27-A  
Sc | 40S ribosomal protein S28-A  
Sd | 40S ribosomal protein S29-A  
Se | 40S ribosomal protein S30-A  
Sf | Ubiquitin-40S ribosomal protein S31  
Sg | Guanine nucleotide-binding protein subunit beta-like protein  
  
Non-standard residues in 6t4q #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
  

> hide atoms

> hide ribbons

> show surfaces

> color gray

> select protein

87780 atoms, 89304 bonds, 4 pseudobonds, 2 models selected  

> color sel white

> select /L*

49852 atoms, 50717 bonds, 35 pseudobonds, 3 models selected  

> color sel #aaffff

> select /S*

37899 atoms, 38533 bonds, 13 pseudobonds, 3 models selected  

> color sel #fad0ff

> select protein sequence .{1}$

548 atoms, 482 bonds, 1 model selected  

> color sel red

> show sel atoms

> select protein sequence w(b)

132 atoms, 138 bonds, 1 model selected  

> color sel green

> show sel atoms

> ~select

Nothing selected  

> view

executed 6T4Q.cxc  

> select /6

1622 atoms, 1811 bonds, 73 pseudobonds, 3 models selected  

> color sel gold

> select /7

1589 atoms, 1773 bonds, 72 pseudobonds, 2 models selected  

> color sel gold

> select /5

644 atoms, 721 bonds, 6 pseudobonds, 2 models selected  

> color sel orange

> close session

> open "C:\bukau_lab\research proposal\ribosome_structure\chimerax\6T4Q.cxc"

> open 6T4Q

6t4q title:  
Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon
combination. [more info...]  
  
Chain information for 6t4q #1  
---  
Chain | Description  
5 | mRNA  
6 | ICG tRNA Arg (P/P)  
7 | tRNA (E/E)  
8 | nascent chain  
C1 | 25S rRNA  
C2 | 18S rRNA  
C3 | 5.8S rRNA  
C4 | 5S rRNA  
LA | 60S ribosomal protein L2-A  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4-A  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6-B  
LF | 60S ribosomal protein L7-A  
LG | 60S ribosomal protein L8-A  
LH | 60S ribosomal protein L9-A  
LI | 60S ribosomal protein L10  
LJ | 60S ribosomal protein L11-B  
LL | 60S ribosomal protein L13-A  
LM | 60S ribosomal protein L14-A  
LN | 60S ribosomal protein L15-A  
LO | 60S ribosomal protein L16-A  
LP | 60S ribosomal protein L17-A  
LQ | 60S ribosomal protein L18-A  
LR | 60S ribosomal protein L19-A  
LS | 60S ribosomal protein L20-A  
LT | 60S ribosomal protein L21-A  
LU | 60S ribosomal protein L22-A  
LV | 60S ribosomal protein L23-A  
LW | 60S ribosomal protein L24-A  
LX | 60S ribosomal protein L25  
LY | 60S ribosomal protein L26-A  
LZ | 60S ribosomal protein L27-A  
La | 60S ribosomal protein L28  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31-A  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L33-A  
Lg | 60S ribosomal protein L34-A  
Lh | 60S ribosomal protein L35-A  
Li | 60S ribosomal protein L36-A  
Lj | 60S ribosomal protein L37-A  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41-A  
Lo | 60S ribosomal protein L42-A  
Lp | 60S ribosomal protein L43-A  
SA | 40S ribosomal protein S0-A  
SB | 40S ribosomal protein S1-A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4-A  
SF | Rps5p  
SG | 40S ribosomal protein S6-A  
SH | 40S ribosomal protein S7-A  
SI | 40S ribosomal protein S8-A  
SJ | 40S ribosomal protein S9-A  
SK | 40S ribosomal protein S10-A  
SL | 40S ribosomal protein S11-A  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14-B  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16-A  
SR | 40S ribosomal protein S17-A  
SS | 40S ribosomal protein S18-A  
ST | 40S ribosomal protein S19-A  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21-A  
SW | 40S ribosomal protein S22-A  
SX | 40S ribosomal protein S23-A  
SY | 40S ribosomal protein S24-A  
SZ | 40S ribosomal protein S25-A  
Sa | 40S ribosomal protein S26-B  
Sb | 40S ribosomal protein S27-A  
Sc | 40S ribosomal protein S28-A  
Sd | 40S ribosomal protein S29-A  
Se | 40S ribosomal protein S30-A  
Sf | Ubiquitin-40S ribosomal protein S31  
Sg | Guanine nucleotide-binding protein subunit beta-like protein  
  
Non-standard residues in 6t4q #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
  

> hide atoms

> hide ribbons

> show surfaces

> color gray

> select protein

87780 atoms, 89304 bonds, 4 pseudobonds, 2 models selected  

> color sel white

> select /L*

49852 atoms, 50717 bonds, 35 pseudobonds, 3 models selected  

> color sel #aaffff

> select /S*

37899 atoms, 38533 bonds, 13 pseudobonds, 3 models selected  

> color sel #fad0ff

> select protein sequence .{1}$

548 atoms, 482 bonds, 1 model selected  

> color sel red

> show sel atoms

> select protein sequence w(b)

132 atoms, 138 bonds, 1 model selected  

> color sel green

> show sel atoms

> color /5-8 gold

> color /Sf,sf,Sg,Lm white

> ~select

Nothing selected  

> view

executed 6T4Q.cxc  

> select /LX

964 atoms, 979 bonds, 1 model selected  

> close session

> open "C:\bukau_lab\research proposal\ribosome_structure\chimerax\6T4Q.cxc"

> open 6T4Q

6t4q title:  
Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon
combination. [more info...]  
  
Chain information for 6t4q #1  
---  
Chain | Description  
5 | mRNA  
6 | ICG tRNA Arg (P/P)  
7 | tRNA (E/E)  
8 | nascent chain  
C1 | 25S rRNA  
C2 | 18S rRNA  
C3 | 5.8S rRNA  
C4 | 5S rRNA  
LA | 60S ribosomal protein L2-A  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4-A  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6-B  
LF | 60S ribosomal protein L7-A  
LG | 60S ribosomal protein L8-A  
LH | 60S ribosomal protein L9-A  
LI | 60S ribosomal protein L10  
LJ | 60S ribosomal protein L11-B  
LL | 60S ribosomal protein L13-A  
LM | 60S ribosomal protein L14-A  
LN | 60S ribosomal protein L15-A  
LO | 60S ribosomal protein L16-A  
LP | 60S ribosomal protein L17-A  
LQ | 60S ribosomal protein L18-A  
LR | 60S ribosomal protein L19-A  
LS | 60S ribosomal protein L20-A  
LT | 60S ribosomal protein L21-A  
LU | 60S ribosomal protein L22-A  
LV | 60S ribosomal protein L23-A  
LW | 60S ribosomal protein L24-A  
LX | 60S ribosomal protein L25  
LY | 60S ribosomal protein L26-A  
LZ | 60S ribosomal protein L27-A  
La | 60S ribosomal protein L28  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31-A  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L33-A  
Lg | 60S ribosomal protein L34-A  
Lh | 60S ribosomal protein L35-A  
Li | 60S ribosomal protein L36-A  
Lj | 60S ribosomal protein L37-A  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41-A  
Lo | 60S ribosomal protein L42-A  
Lp | 60S ribosomal protein L43-A  
SA | 40S ribosomal protein S0-A  
SB | 40S ribosomal protein S1-A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4-A  
SF | Rps5p  
SG | 40S ribosomal protein S6-A  
SH | 40S ribosomal protein S7-A  
SI | 40S ribosomal protein S8-A  
SJ | 40S ribosomal protein S9-A  
SK | 40S ribosomal protein S10-A  
SL | 40S ribosomal protein S11-A  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14-B  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16-A  
SR | 40S ribosomal protein S17-A  
SS | 40S ribosomal protein S18-A  
ST | 40S ribosomal protein S19-A  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21-A  
SW | 40S ribosomal protein S22-A  
SX | 40S ribosomal protein S23-A  
SY | 40S ribosomal protein S24-A  
SZ | 40S ribosomal protein S25-A  
Sa | 40S ribosomal protein S26-B  
Sb | 40S ribosomal protein S27-A  
Sc | 40S ribosomal protein S28-A  
Sd | 40S ribosomal protein S29-A  
Se | 40S ribosomal protein S30-A  
Sf | Ubiquitin-40S ribosomal protein S31  
Sg | Guanine nucleotide-binding protein subunit beta-like protein  
  
Non-standard residues in 6t4q #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
  

> hide atoms

> hide ribbons

> show surfaces

> color gray

> color protein white

> color /L* #aaffff

> color /S* #fad0ff

> color /LX,LO #00aaff

> select protein sequence .{1}$

548 atoms, 482 bonds, 1 model selected  

> color sel red

> show sel atoms

> select protein sequence w(b)

132 atoms, 138 bonds, 1 model selected  

> color sel green

> show sel atoms

> color /5-8 gold

> color /Sf,sf,Sg,Lm white

> ~select

Nothing selected  

> view

executed 6T4Q.cxc  

> toolshed show "Side View"

> lighting simple

> select /SM

875 atoms, 883 bonds, 1 model selected  

> select /SM

875 atoms, 883 bonds, 1 model selected  

> select /SC

1626 atoms, 1656 bonds, 1 model selected  

> select /LR

1517 atoms, 1532 bonds, 1 pseudobond, 2 models selected  

> select /LI

1764 atoms, 1801 bonds, 1 model selected  

> select /Lk

612 atoms, 618 bonds, 1 model selected  

> select /Lk

612 atoms, 618 bonds, 1 model selected  

> select /LD

2351 atoms, 2400 bonds, 1 model selected  

> select /Le

1019 atoms, 1038 bonds, 4 pseudobonds, 2 models selected  

> select /LB

3077 atoms, 3146 bonds, 2 pseudobonds, 2 models selected  

> select /Ll

436 atoms, 443 bonds, 1 model selected  

> select /La

1174 atoms, 1204 bonds, 1 pseudobond, 2 models selected  

> select /Lb

462 atoms, 473 bonds, 1 model selected  

> select /LX

964 atoms, 979 bonds, 1 model selected  

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> show sel atoms

> show sel atoms

> hide sel surfaces

> style sel stick

Changed 1729 atom styles  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /SK PRO 88 N  

187 hydrogen bonds found  

> select /Sg

2383 atoms, 2436 bonds, 1 model selected  

> show sel atoms

> hide sel surfaces

> style sel stick

Changed 2383 atom styles  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> select up

1729 atoms, 1754 bonds, 2 models selected  

> select down

12 atoms, 12 bonds, 2 models selected  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /SK PRO 88 N  

1 hydrogen bonds found  

> ui mousemode rightMode label

> label #1/SD:225

> style sel ball

Changed 12 atom styles  

> color sel byhetero

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> select /SD:225@CA

1 atom, 1 model selected  

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> show sel surfaces

> select /Sg

2383 atoms, 2436 bonds, 1 model selected  

> show sel surfaces

> select /SD:225@C

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> hide sel surfaces

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> ui mousemode rightMode label

> label delete residues

> 2dlabels S3

> 2dlabels text S3

> label #1/SR:23

> ui mousemode rightMode "move label"

> 2dlabels #2.1 xpos 0.468 ypos 0.502

> hide #1.8 models

> select clear

> view

> 2dlabels #2.1 xpos 0.338 ypos 0.405

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> style sel ball

Changed 1729 atom styles  

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select clear

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

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

> color sel indigo

> show sel surfaces

> 2dlabels #2.1 xpos 0.330 ypos 0.425

> select /SD:225@OH

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> color sel red

> select clear

> 2dlabels text uS3 color red

> close #2.1

> 2dlabels #2.2 xpos 0.319 ypos 0.448

> 2dlabels text uS3 color red bgColor black

> close #2.1

> undo

> undo

> redo

> close #2

> 2dlabels text uS3 color red bgColor black

> 2dlabels #2.1 xpos 0.311 ypos 0.423

> select clear

> 2dlabels #2.1 xpos 0.316 ypos 0.467

> save C:\Users\Shiran\Desktop\image2.png supersample 3

> save C:\Users\Shiran\Desktop\uS3.png supersample 5

> 2dlabels #2.1 xpos 0.316 ypos 0.467

> hide #!2 models

> select /SD:225@CE1

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> hide sel surfaces

> select /SD:224@O

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 2 models selected  

> hide sel surfaces

> select /SD:225@O

1 atom, 1 model selected  

> color sel blue

> select clear

> select /SD:225@CB

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> label sel color red bgColor black

Expected a keyword  

> label sel color red bgColor black size 50

> label defaultHeight 50

> label defaultHeight 28.0

Invalid "size" argument: Expected 'default' or an integer  

> label sel color red bgColor black size 50

> label delete

> label sel color red bgColor black size 50

> label delete

> label sel color red bgColor black size 25

> label delete

> label defaultHeight 25

> label defaultHeight 25.0

> label sel color red bgColor black size 25

> label delete

> label sel color red bgColor black size 10

> label delete

> label sel color red bgColor black size 10 defaultHeight 10

> label defaultHeight 10.0

> label sel color red bgColor black size 50 defaultHeight 10

> label sel color red bgColor black size 50 defaultHeight 5

> label defaultHeight 5.0

> label delete

> label sel color red bgColor black size 50 defaultHeight 5

> label delete

> label sel color red bgColor black size 50 defaultHeight 5 onTop false

> label sel color red bgColor black size 25 defaultHeight 5 onTop false

> label delete

> label sel color red bgColor black size 25 defaultHeight 5 onTop false

> label sel color red bgColor black size 10 defaultHeight 5 onTop false

> label delete

> label sel color red bgColor black size 10 defaultHeight 5 onTop false

> label sel color red bgColor black size 10 defaultHeight 1 onTop false

> label defaultHeight 1.0

> label delete

> label sel color red bgColor black size 10 defaultHeight 1 onTop false

> label sel color red bgColor black size 10 defaultHeight 3 onTop false

> label defaultHeight 3.0

> label delete

> label sel color red bgColor black size 10 defaultHeight 3 onTop false

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> select /SD:225@O

1 atom, 1 model selected  

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> label sel atoms color red bgColor black size 50 defaultHeight 3 onTop false

> label delete

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> select clear

> save C:\Users\Shiran\Desktop\uS3_zoom.png supersample 5

> select up

2 atoms, 1 bond, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> select up

1729 atoms, 1754 bonds, 2 models selected  

> color sel #fad0ff

> show sel surfaces

> label delete

> select /SD:225@CE2

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> color sel red

> select /SM

875 atoms, 883 bonds, 1 model selected  

> color sel indigo

> select /SM:143@O

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 2 models selected  

> color sel red

> hide sel surfaces

> style sel ball

Changed 9 atom styles  

> select up

875 atoms, 883 bonds, 2 models selected  

> hide sel surfaces

> show sel atoms

> style sel ball

Changed 875 atom styles  

> show sel surfaces

> select down

9 atoms, 8 bonds, 2 models selected  

> select clear

> 2dlabels text eS12 color red bgColor black

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> 2dlabels #2.2 xpos 0.332 ypos 0.304

> save C:\Users\Shiran\Desktop\eS12.png supersample 5

> close #2

> select /SM:143@O

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 2 models selected  

> hide sel surfaces

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /SK PRO 88 N  

0 hydrogen bonds found  

> select /SM:143@O

1 atom, 1 model selected  

> color sel blue

> select up

9 atoms, 8 bonds, 2 models selected  

> select up

875 atoms, 883 bonds, 2 models selected  

> select up

203559 atoms, 218508 bonds, 2 models selected  

> select up

203559 atoms, 218508 bonds, 418 pseudobonds, 85 models selected  

> select down

203559 atoms, 218508 bonds, 83 models selected  

> select down

875 atoms, 883 bonds, 83 models selected  

> select down

9 atoms, 8 bonds, 2 models selected  

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> ui mousemode rightMode "move label"

> select clear

> select up

Nothing selected  

> save C:\Users\Shiran\Desktop\eS12_zoom.png supersample 5

> label delete

> select /SM:143@CA

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 2 models selected  

> select up

875 atoms, 883 bonds, 2 models selected  

> show sel surfaces

> color sel #fad0ff

> select /SM:143@O

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 2 models selected  

> color sel red

> select /SM

875 atoms, 883 bonds, 1 model selected  

> select /SN

1192 atoms, 1215 bonds, 1 model selected  

> select /SP

916 atoms, 936 bonds, 1 model selected  

> select /SC

1626 atoms, 1656 bonds, 1 model selected  

> color sel indigo

> select /SC:249@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> color sel red

> 2dlabels text uS5 color red bgColor black

> 2dlabels #2.1 xpos 0.466 ypos 0.246

> select clear

> save C:\Users\Shiran\Desktop\uS5.png supersample 5

> close #2

> select /SC:249@O

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> hide sel surfaces

> style sel ball

Changed 5 atom styles  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /SK PRO 88 N  

0 hydrogen bonds found  

> select up

39 atoms, 38 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 39 atom styles  

> select up

1626 atoms, 1656 bonds, 2 models selected  

> style sel ball

Changed 1626 atom styles  

> show sel atoms

> select /SC:249@O

1 atom, 1 model selected  

> color sel blue

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

39 atoms, 38 bonds, 2 models selected  

> hide sel surfaces

> select down

5 atoms, 4 bonds, 2 models selected  

> select up

39 atoms, 38 bonds, 2 models selected  

> select down

5 atoms, 4 bonds, 2 models selected  

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> select clear

> save C:\Users\Shiran\Desktop\uS5_zoom.png supersample 5

> label delete

> select /SC:249@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

39 atoms, 38 bonds, 2 models selected  

> select up

1626 atoms, 1656 bonds, 2 models selected  

> hide sel atoms

> show sel surfaces

> color sel #fad0ff

> select down

39 atoms, 38 bonds, 2 models selected  

> select down

5 atoms, 4 bonds, 2 models selected  

> color sel red

> select /SU

797 atoms, 807 bonds, 1 model selected  

> color sel indigo

> select /SU:119@CB

1 atom, 1 model selected  

> color sel red

> 2dlabels text uS10 color red bgColor black

> 2dlabels #2.1 xpos 0.629 ypos 0.646

> select clear

> 2dlabels #2.1 xpos 0.567 ypos 0.608

> 2dlabels #2.1 xpos 0.563 ypos 0.551

> 2dlabels #2.1 xpos 0.518 ypos 0.673

> 2dlabels #2.1 xpos 0.516 ypos 0.631

> save C:\Users\Shiran\Desktop\uS10.png supersample 5

> close #2

> select /SU:119@CB

1 atom, 1 model selected  

> hide sel surfaces

> select up

5 atoms, 4 bonds, 2 models selected  

> hide sel surfaces

> style sel ball

Changed 5 atom styles  

> select up

797 atoms, 807 bonds, 2 models selected  

> select down

5 atoms, 4 bonds, 2 models selected  

> select up

797 atoms, 807 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 797 atom styles  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /SK PRO 88 N  

99 hydrogen bonds found  

> select down

5 atoms, 4 bonds, 2 models selected  

> interfaces sel & ~solvent

0 buried areas:  

> color sel red

> select /SU:119@O

1 atom, 1 model selected  

> color sel blue

> select clear

> select up

2 atoms, 1 bond, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> label sel color red bgColor black size 50 defaultHeight 3 onTop false

> select clear

> save C:\Users\Shiran\Desktop\uS10_zoom.png supersample 5

> label delete

> select /SU:119@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

797 atoms, 807 bonds, 2 models selected  

> color sel #fad0ff

> show sel surfaces

> hide sel atoms

> select down

5 atoms, 4 bonds, 2 models selected  

> select down

1 atom, 2 models selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> color sel red

> select /SP

916 atoms, 936 bonds, 1 model selected  

> select /SD

1729 atoms, 1754 bonds, 1 model selected  

> close session

Missing or invalid "filename" argument: Expected a file name  

Unknown command: 6U5T  

> open 6U5T

Summary of feedback from opening 6U5T fetched from pdb  
---  
notes | Fetching compressed mmCIF 6u5t from
http://files.rcsb.org/download/6u5t.cif  
Fetching CCD PNS from http://ligand-expo.rcsb.org/reports/P/PNS/PNS.cif  
Fetching CCD FMN from http://ligand-expo.rcsb.org/reports/F/FMN/FMN.cif  
  
6u5t title:  
Electron cryomicroscopy Structure of S. cerevisiae FAS in the Apo state [more
info...]  
  
Chain information for 6u5t #1  
---  
Chain | Description  
A | Fatty acid synthase subunit α  
G | Fatty acid synthase subunit β  
  
Non-standard residues in 6u5t #1  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
PNS — 4'-phosphopantetheine  
  
6u5t mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  
  

> select /A

12207 atoms, 12429 bonds, 3 pseudobonds, 2 models selected  

> color sel #b22222

> select /G

16026 atoms, 16393 bonds, 1 pseudobond, 2 models selected  

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

> color sel navy

> select strand

3718 atoms, 3690 bonds, 1 model selected  

> select coil

10558 atoms, 10569 bonds, 4 pseudobonds, 2 models selected  

> select /A&coil

4775 atoms, 4780 bonds, 3 pseudobonds, 2 models selected  

> toolshed show "Cage Builder"

> view

> preset "overall look" interactive

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 405, in _background_color_changed  
l.update_drawing()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 495, in update_drawing  
d.needs_update = True  
AttributeError: 'NoneType' object has no attribute 'needs_update'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'needs_update'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 495, in update_drawing  
d.needs_update = True  
  
See log for complete Python traceback.  
  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> set bgColor white

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 405, in _background_color_changed  
l.update_drawing()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 495, in update_drawing  
d.needs_update = True  
AttributeError: 'NoneType' object has no attribute 'needs_update'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'needs_update'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\label\label2d.py", line 495, in update_drawing  
d.needs_update = True  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 432.00
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Graphics
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → 'NoneType' object has no attribute 'needs_update' after 2D labels closed

comment:2 by Eric Pettersen, 6 years ago

Resolution:	→ fixed
Status:	accepted → closed

Hi Shiran,

This bug was fixed just yesterday, so if you get the current daily build you shouldn't encounter it any more. Alternatively, you can work around the bug by using "2dlabels del all" to delete all labels before using "close" to close all models.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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