Ribbon going through RNA adduct instead of base

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202311052311 (2023-11-05 23:11:54 UTC)
Description
Nucleic acid cartoon drawing goes wonky through the non-standard RNA base 12A - spline is going through the CA atom of a threonine adduct on the base, introducing a huge kink.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7.dev202311052311 (2023-11-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6sgc

6sgc title:  
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]  
  
Chain information for 6sgc #1  
---  
Chain | Description | UniProt  
23 33 | tRNA (Lys3) |  
54 | 28S ribosomal RNA |  
74 | 5S ribosomal RNA |  
84 | 5.8S ribosomal RNA |  
A1 | 18S ribosomal RNA |  
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257  
B | Ribosomal protein | G1SKZ8_RABIT 1-217  
B1 | uS2 |  
B2 | uL3 | G1TL06_RABIT 2-403  
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264  
C2 | uL4 |  
D1 | uS5 |  
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297  
E1 | uS5 | G1TNM3_RABIT 1-243  
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291  
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263  
F2 | uL30 | G1TUB1_RABIT 1-247  
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204  
G2 | eL8 |  
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249  
H2 | uL6 | G1TX33_RABIT 1-192  
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194  
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214  
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208  
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178  
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194  
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165  
L2 | eL13 |  
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158  
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218  
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132  
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204  
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151  
O2 | uL13 |  
P1 | uS11 |  
P2 | uL22 | G1TVT6_RABIT 1-184  
Q1 | uS19 | G1U0Q2_RABIT 1-145  
Q2 | eL18 |  
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146  
R2 | eL19 |  
S1 | eS17 | G1TU13_RABIT 1-135  
S2 | eL20 |  
T1 | eS13 | G1TPG3_RABIT 1-152  
T2 | eL21 | G1SHQ2_RABIT 1-160  
U1 | eS19 | G1TN62_RABIT 1-145  
U2 | eL22 |  
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119  
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140  
W1 | eS21 |  
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157  
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130  
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156  
XX | poly-lysine nascent chain |  
Y1 | uS12 |  
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145  
Z1 | eS24 |  
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136  
a1 | eS25 | G1TDB3_RABIT 1-125  
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148  
b1 | eS26 |  
b2 | eL29 |  
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84  
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115  
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69  
d2 | eL31 | G1SHG0_RABIT 1-125  
e1 | uS14 | G1U7M4_RABIT 1-56  
e2 | eL32 | G1U437_RABIT 1-135  
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132  
f2 | eL33 | G1SF08_RABIT 1-110  
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156  
g2 | eL34 | G1U945_RABIT 1-116  
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317  
h2 | uL29 | G1SIT5_RABIT 1-123  
i1 | polyA mRNA |  
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105  
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97  
k2 | eL38 | G1U001_RABIT 1-70  
l2 | eL39 | G1TTN1_RABIT 1-51  
m2 | eL40 |  
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25  
o2 | eL42 | G1U344_RABIT 1-106  
p2 | eL43 | G1SY53_RABIT 1-92  
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137  
s2 | uL10 |  
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165  
  
Non-standard residues in 6sgc #1  
---  
MG — magnesium ion  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  

> cartoon

> style stick

Changed 218966 atom styles  

> color byhetero

> view /23:37




OpenGL version: 3.3.0 NVIDIA 529.08
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
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Qt platform: windows

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Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
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CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
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[Tristan Croll]

Confirming the obvious: changing the name of the CA to something else ("CA99") and redrawing the cartoon leads to a correct ribbon path.

[Tom Goddard]

Fixed in daily build and 1.7 release candidate.

The ribbon code just looked for atoms CA or C5' or P and did not consider whether the residue polymer type was amino acid or nucleic acid. I made it only use CA if the polymer type is amino acid and only use C5' or P if the polymer type is nucleic acid.