Opened 5 years ago

Closed 4 years ago

#3237 closed defect (fixed)

nucleotides disconnected

Reported by: sitins07@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-05-07)
Description
Wrong visualization of the CIF file of the nucleic acid. Residues are separates, but they should be connected. File is the output from Phenix real space refine. 

Log:
UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open X:/Work/Projects/48S/ChimeraX/closed/a-tRNAi/Met-tRNAi-6ek0.cif-
> coot-4.pdb

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/a-tRNAi/Met-tRNAi-6ek0.cif-coot-4.pdb  
---  
warning | Ignored bad PDB record found on line 1651  
END  
  
Chain information for Met-tRNAi-6ek0.cif-coot-4.pdb #1  
---  
Chain | Description  
a | No description available  
  

> open X:/Work/Projects/48S/ChimeraX/closed/3d360_closedagain_c3_ctf_37A.ccp4

Opened 3d360_closedagain_c3_ctf_37A.ccp4, grid size 360,360,360, pixel 1.16,
shown at level 4.12, step 2, values float32  

> volume #2 step 1

> select #1

1604 atoms, 1795 bonds, 1 model selected  

> volume zone #2 nearAtoms sel range 5

> volume zone #2 nearAtoms sel range 5 newMap true

> volume unzonezone #2

Expected a density maps specifier or a keyword  

> volume unzone #2

> volume #3 color #ffffb0

> volume #3 color #ffffb2

> volume #3 color #ffffb9

> volume #3 color #fffccb

> volume #3 color #fffcf2

> volume #3 color white

> volume #3 color #fdfdfd

> volume #3 color #fcfcfc

> volume #3 color #f8f8f8

> volume #3 color #f0f0f0

> volume #3 color #e2e2e2

> volume #3 color #d4d4d4

> volume #3 color #cacaca

> volume #3 color #c3c3c3

> volume #3 color #bfbfbf

> volume #3 color #bebebe

> volume #3 color #bdbdbd

> volume #3 color #bcbcbc

> volume #3 color #bababa

> volume #3 color #bababa01

> volume #3 color #bababa0f

> volume #3 color #bababa96

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1604 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1604 atom styles  

> ui mousemode right select

> select clear

> hide cartoons

> select clear

> volume #3 level 4.61

> volume #3 level 9.796

> close #1

> open X:/Work/Projects/48S/ChimeraX/closed/a-tRNAi/Met-tRNAi-6ek0.cif-
> coot-5.pdb

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/a-tRNAi/Met-tRNAi-6ek0.cif-coot-5.pdb  
---  
warning | Ignored bad PDB record found on line 1651  
END  
  
Chain information for Met-tRNAi-6ek0.cif-coot-5.pdb #1  
---  
Chain | Description  
a | No description available  
  

> hide cartoons

> nucleotides fill

> style nucleic stick

Changed 1604 atom styles  

> hide #!3 models

> show #!2 models

> open X:/Work/Projects/48S/ChimeraX/closed/40S/h40S_orig_6ek0_closed.pdb

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/40S/h40S_orig_6ek0_closed.pdb  
---  
warnings | Bad residue range for secondary structure: HELIX 4 4 MET S 1 LYS S
227 1 227  
Bad residue range for secondary structure: HELIX 13 13 MET S 1 ARG S 146 1 146  
Bad residue range for secondary structure: HELIX 16 16 PRO S 2 LYS S 144 1 143  
Bad residue range for secondary structure: HELIX 17 17 ALA S 16 ALA S 119 1
104  
Bad residue range for secondary structure: HELIX 29 29 PRO S 2 GLY S 186 1 185  
12 messages similar to the above omitted  
  
Chain information for h40S_orig_6ek0_closed.pdb #4  
---  
Chain | Description  
L | No description available  
S | No description available  
S | No description available  
  

> close #4

> open 6ek0

6ek0 title:  
High-resolution cryo-EM structure of the human 80S ribosome [more info...]  
  
Chain information for 6ek0 #4  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
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 ribosomal RNA  
S6 | Human initiator Met-tRNA-i  
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 6ek0 #4  
---  
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  
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)  
MG — magnesium ion  
ZN — zinc ion  
  

> hide atoms

> show cartoons

> select #4

219534 atoms, 235413 bonds, 5578 pseudobonds, 4 models selected  

> cd X:/Work/Projects/48S/ChimeraX/closed/40S

Current working directory is: X:\Work\Projects\48S\ChimeraX\closed\40S  

> save 40S.pdb models #4

> save 40S.pdb models #4

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S.pdb

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/40S/40S.pdb  
---  
warnings | Ignored bad PDB record found on line 226716  
END  
  
Bad residue range for secondary structure: HELIX 12 12 THR L 189 ARG L 200 1
12  
Bad residue range for secondary structure: HELIX 19 19 ASN L 116 ALA L 129 1
14  
Bad residue range for secondary structure: HELIX 36 36 ASN L 9 LYS L 14 1 6  
Bad residue range for secondary structure: HELIX 46 46 ILE L 227 VAL L 231 1 5  
Bad residue range for secondary structure: HELIX 49 49 SER L 58 LYS L 66 1 9  
254 messages similar to the above omitted  
  
Chain information for 40S.pdb #5  
---  
Chain | Description  
L | No description available  
L | No description available  
S | No description available  
S | No description available  
  

> ui mousemode right "rotate selected models"

> close #5

> save 40S.cif models #4

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S-1.cif

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/40S/40S-1.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 20219  
Unknown polymer entity '4' near line 20509  
Unknown polymer entity '49' near line 22408  
Unknown polymer entity '5' near line 24149  
Unknown polymer entity '50' near line 27394  
Unknown polymer entity '1' near line 29132  
76 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 40S-1.cif #5  
---  
Chain | Description  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Lz | No description available  
S2 | No description available  
S6 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
  

> ui mousemode right select

Drag select of 2 3d360_closedagain_c3_ctf_37A.ccp4 , 6 pseudobonds, 1312
residues, 13859 atoms  

> select #5

219534 atoms, 235413 bonds, 34 pseudobonds, 2 models selected  

> hide #!5 models

> hide #!4 models

Drag select of  

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S-1.cif

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/40S/40S-1.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 20219  
Unknown polymer entity '4' near line 20509  
Unknown polymer entity '49' near line 22408  
Unknown polymer entity '5' near line 24149  
Unknown polymer entity '50' near line 27394  
Unknown polymer entity '1' near line 29132  
76 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 40S-1.cif #6  
---  
Chain | Description  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Lz | No description available  
S2 | No description available  
S6 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
  

> select #5

219534 atoms, 235413 bonds, 34 pseudobonds, 2 models selected  

> close #5

> close #4

> close #6

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S.cif

Chain information for 40S.cif #4  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
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 ribosomal RNA  
S6 | Human initiator Met-tRNA-i  
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  
  

> open X:/Work/Projects/48S/Phenix/RealSpaceRefine_19/Met-tRNAi-6ek0.cif-
> coot-2_real_space_refined_real_space_refined.cif

Summary of feedback from opening
X:/Work/Projects/48S/Phenix/RealSpaceRefine_19/Met-tRNAi-6ek0.cif-
coot-2_real_space_refined_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 145  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "A" near line 172  
Skipping chem_comp category: Missing column 'type' near line 2052  
Skipping chem_comp category: Missing column 'type' near line 2337  
Skipping chem_comp category: Missing column 'type' near line 2598  
Skipping chem_comp category: Missing column 'type' near line 2850  
  

> hide #!4 models

> hide #!2 models

> hide #1 models

Drag select of 1604 atoms, 50 pseudobonds, 1721 bonds  
Drag select of 1604 atoms, 50 pseudobonds, 1721 bonds  

> save trna-test.cif models #5

> open X:/Work/Projects/48S/ChimeraX/closed/40S/trna-test.cif

Summary of feedback from opening
X:/Work/Projects/48S/ChimeraX/closed/40S/trna-test.cif  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "A" near line 118  
  

> hide #!5 models

> close #6

> close #1#2-4

> close session

> open X:/Work/Projects/48S/Phenix/RealSpaceRefine_19/Met-tRNAi-6ek0.cif-
> coot-2_real_space_refined_real_space_refined.cif

Summary of feedback from opening
X:/Work/Projects/48S/Phenix/RealSpaceRefine_19/Met-tRNAi-6ek0.cif-
coot-2_real_space_refined_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 145  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "A" near line 172  
Skipping chem_comp category: Missing column 'type' near line 2052  
Skipping chem_comp category: Missing column 'type' near line 2337  
Skipping chem_comp category: Missing column 'type' near line 2598  
Skipping chem_comp category: Missing column 'type' near line 2850  
  




OpenGL version: 3.3.0 NVIDIA 445.87
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 18363)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
File attachment: Screenshot_26546.png

Screenshot_26546.png​

Attachments (1)

Screenshot_26546.png​ (519.3 KB ) - added by sitins07@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (9)

by sitins07@…, 5 years ago

Attachment: Screenshot_26546.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → nucleotides disconnected

comment:2 by Greg Couch, 5 years ago

Status: assigned → feedback

Can you supply the data file that causes the problems? If you don't want it publicly visible in the ticket, email it directly to me at gregc@….

The problem is due to the missing sequence information in the file, i.e., the entity_poly_seq information, so ChimeraX has to guess which residues are in a chain. The guessing works fairly well for amino acids, so this shouldn't be too hard. If you took your structure and used Phenix's tool to add the missing (sequence) mmCIF information for submission to the PDB, then ChimeraX would know how to connect them.

comment:3 by Greg Couch, 5 years ago

Perhaps I spoke too soon. Seeing your data file will help tremendously. I'm curious about what caused the "Unable to infer polymer connectivity due to unspecified label_seq_id for residue "A" near line 172" error. If there are no sequence numbers, that will require even more guessing.

comment:4 by Greg Couch, 5 years ago

Thanks for the structure. I will make it work. Might add a popup saying "this is an extremely bad mmCIF file, proceed?". Just joking.

in reply to:  6 comment:5 by sitins07@…, 5 years ago 

Cool. thanks!
Why it is so? I only started to work with mmCIF files, so can't really get
what is wrong with it.

Respectfully yours,
Valentyn Petrychenko


чт, 21 трав. 2020 о 20:43 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:

comment:6 by Greg Couch, 5 years ago

The problem is that it is an underspecified mmCIF file. I can't speak for the Phenix folks, but my guess it is because it represents an intermediate version, and the complete version is generated by post-processing the intermediate version with the mmtbx.prepare_pdb_deposition program (see ​https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html). If you post-processed your mmCIF, then ChimeraX would be *much* happier. Regardless, this is an important "use case", so I'll get it to work. ChimeraX might make a bad guess about the connectivity since the sequence information is missing, but it should be connected.

in reply to:  8 comment:7 by sitins07@…, 5 years ago 

Awesome, thanks!

Respectfully yours,
Valentyn Petrychenko


чт, 21 трав. 2020 о 23:37 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:

comment:8 by Greg Couch, 4 years ago

Resolution: → fixed
Status: feedback → closed

This is finally fixed in the daily build. And will be in the next 1.2 release candidate (1.2.5).

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