Nucleotides: 'N' not in standard_bases

[dborgesrmit@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.9 (2019-05-16)
Description
#Color, style, and save 40S proteins/nucleotides
#18S (40S) rRNA : chain S2
nucleotides /S2 ladder
style /S2 sphere
show /S2 atoms
color /S2 chartreuse

Log:
UCSF ChimeraX version: 0.9 (2019-05-16)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6qzp

6qzp title:  
High-resolution cryo-EM structure of the human 80S ribosome [more info...]  
  
Chain information for 6qzp #1  
---  
Chain | Description  
L5 | 28S rRNA (3773-MER)  
L7 | 5S rRNA (120-MER)  
L8 | 5.8S rRNA (156-MER)  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18a  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10a  
S2 | 18S rRNA (1740-MER)  
S6 | E site tRNA (75-MER)  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
  
Non-standard residues in 6qzp #1  
---  
B8H —
[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
B8T — 4-methyl, cytidine-5'-monophosphate  
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)  
HYG — hygromycin B (hygromix, antihelmycin, hydromycin B, destomysin,
antibiotic A-396-II)  
M7A — 7-methyl, adenosine-5'-monophosphate  
MG — magnesium ion  
ZN — zinc ion  
  
  

> ~hbonds

> hide #!1.2 models

> hide atoms

> nucleotides /S6 fill

> style /S6 ball

Changed 1604 atom styles  

> show /S6 atoms

> color /S6 fuchsia

> save D:/Euplotid/raw_models/EtRNA.obj format obj

> hide /S6

> nucleotides /S2 ladder

> style /S2 sphere

Changed 37126 atom styles  

> show /S2 atoms

Traceback (most recent call last):  
File "D:\software\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py",
line 130, in invoke  
return self._func(self._name, data)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 654, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
KeyError: 'N'  
  
Error processing trigger "changes": 'N':  
KeyError: 'N'  
  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
  
See log for complete Python traceback.  
  

> color /S2 chartreuse

Traceback (most recent call last):  
File "D:\software\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py",
line 130, in invoke  
return self._func(self._name, data)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 654, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
KeyError: 'N'  
  
Error processing trigger "changes": 'N':  
KeyError: 'N'  
  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\software\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py",
line 130, in invoke  
return self._func(self._name, data)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 501, in rebuild  
_rebuild_molecule('internal', mol)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 654, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
KeyError: 'N'  
  
Error processing trigger "new frame": 'N':  
KeyError: 'N'  
  
File "D:\software\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1225, in make_ladder  
is_purine = standard_bases[name]['tag'] == PURINE  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13543 Core Profile Forward-Compatible Context 25.20.15002.58
OpenGL renderer: Radeon RX Vega
OpenGL vendor: ATI Technologies Inc.

[Greg Couch]

Fixed it.