Opened 5 months ago

Closed 5 months ago

Last modified 5 months ago

#18017 closed defect (fixed)

Non-chain-forming bond merges chains

Reported by: psauer@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Unintended chain ID change: when creating a covalent bond between /NC:31@C and /Pt:75@O3' (a tRNA-peptide bond in a ribosome), the chain ID of  /Pt is changed to /NC. This should not happen. Not sure if this is because my cif file is weird or if it is a bug. Thanks 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> open
> /Users/psauer/Documents/Processing/ChimeraX_startup_preferences_Paul_20240911.cxc

> camera ortho

> cofr centerOfView

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  

> alias hh hide H

> name roi (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) | (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) :<2.5 & :HOH

> name miniroi (/Pt:74-end /NC:21-end /By:21-end /X)

> name froi :3905,3907,3908,4397,4398,3909,4449,5167,5394,5258 :<2.5 & :HOH | (:3905,3907,3908,4397,4398,3909,4449,5167,5394,5258)

> name broi :4398,4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303 :<2.5 & :HOH | (:4398, 4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303)

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 8 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 60; volume step 1

> alias paulunclip ~clip; transparency 0; lighting soft; view all

> alias paulambience lighting fillInt 0.2 ambientInt 1.2 intensity 0.2
> multishadow 256 shadows false

> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon; lighting intens 0.3

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias paulvis lighting fillInt 0.2 ambientInt 1.2 intensity 0.2 multishadow
> 256 shadows false; material transparentcastshadows false; style $1 stick;
> transparency $1 60; nucleotides $1 atom; hide $1 cartoon; show $1 atoms;
> hide H; paulcolor $1

> alias paullabel label $* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH; label $*:IDB* text IDB

> alias IDB view :IDB*; paulclip; volume step 1

> alias nucrib cartoon style nucleic xsect oval width 2 thick 2

> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/Et*
> #b2df8a; color $*/mR #e31a1c; color $*:ANM $*:IDB* yellow; color $*/By,NC
> #fb9a99; color $*:Mg,K,Zn byhetero; color $*:HOH byhetero

> alias center cofron; view $* clip t pad 0.5; select $*

> alias paulrenumber renumber $1/L5 &~ nucleic start 10000 rel f; renumber
> $1/L5:K start 5100 rel f; renumber $1/L5:MG start 5300 rel f; renumber $1/L5
> & ligand start 5600 rel f; renumber $1/L5:IDB start 5700 rel f; renumber
> $1/L5:HOH start 6000 rel f

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_30

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add IDB command IDB

> buttonpanel Shortcuts add paulvis command "paulvis #*"

> buttonpanel Shortcuts add paullabel command paullabel

> buttonpanel Shortcuts add paulclip command paulclip

> buttonpanel Shortcuts add paullight command paullight

> buttonpanel Shortcuts add paulsave command paulsave

> buttonpanel Shortcuts add unclip command paulunclip

> buttonpanel Shortcuts add paulambience command paulambience

> buttonpanel Shortcuts add paulstyle command paulstyle

> buttonpanel Shortcuts add delete_selected command "delete sel"

executed ChimeraX_startup_preferences_Paul_20240911.cxc  

> alias oo open
> /Users/psauer/Documents/Processing/ChimeraX_startup_preferences_Paul_20240911.cxc

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/PDB_deposition/noIDB_MYC_model_refined_060.cif

Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
PS2/PDB_deposition/noIDB_MYC_model_refined_060.cif  
---  
warnings | Unknown polymer entity '1' on line 463  
Unknown polymer entity '2' on line 80137  
Unknown polymer entity '3' on line 82726  
Unknown polymer entity '4' on line 86126  
Unknown polymer entity '5' on line 88141  
77 messages similar to the above omitted  
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61  
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for noIDB_MYC_model_refined_060.cif #1  
---  
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  
NC | No description available  
Pt | No description available  
S2 | 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  
mR | No description available  
  
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> style stick

Changed 216956 atom styles  

> cofron

> paulclip

Changed 216956 atom styles  

> surface cap false

No volumes specified  

> close #1

> close session

> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif

Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 19  
Unknown polymer entity '1' on line 114  
Unknown polymer entity '2' on line 79828  
Unknown polymer entity '3' on line 82417  
Unknown polymer entity '4' on line 85817  
Unknown polymer entity '5' on line 87832  
77 messages similar to the above omitted  
Expected gap or linking atom in AME /SV:1 for GLN /SV:2  
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61  
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for noIDB_MYC_model_refined_060_altconf-coot.cif #1  
---  
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  
NC | No description available  
Pt | No description available  
S2 | 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  
mR | No description available  
  
62 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> style stick

Changed 216956 atom styles  

> oo

> open
> /Users/psauer/Documents/Processing/ChimeraX_startup_preferences_Paul_20240911.cxc

> camera ortho

> cofr centerOfView

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  

> alias hh hide H

> name roi (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) | (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) :<2.5 & :HOH

> name miniroi (/Pt:74-end /NC:21-end /By:21-end /X)

> name froi :3905,3907,3908,4397,4398,3909,4449,5167,5394,5258 :<2.5 & :HOH | (:3905,3907,3908,4397,4398,3909,4449,5167,5394,5258)

> name broi :4398,4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303 :<2.5 & :HOH | (:4398, 4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303)

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 8 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 60; volume step 1

> alias paulunclip ~clip; transparency 0; lighting soft; view all

> alias paulambience lighting fillInt 0.2 ambientInt 1.2 intensity 0.2
> multishadow 256 shadows false

> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon; lighting intens 0.3

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias paulvis lighting fillInt 0.2 ambientInt 1.2 intensity 0.2 multishadow
> 256 shadows false; material transparentcastshadows false; style $1 stick;
> transparency $1 60; nucleotides $1 atom; hide $1 cartoon; show $1 atoms;
> hide H; paulcolor $1

> alias paullabel label $* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH; label $*:IDB* text IDB

> alias IDB view :IDB*; paulclip; volume step 1

> alias nucrib cartoon style nucleic xsect oval width 2 thick 2

> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/Et*
> #b2df8a; color $*/mR #e31a1c; color $*:ANM $*:IDB* yellow; color $*/By,NC
> #fb9a99; color $*:Mg,K,Zn byhetero; color $*:HOH byhetero

> alias center cofron; view $* clip t pad 0.5; select $*

> alias paulrenumber renumber $1/L5 &~ nucleic start 10000 rel f; renumber
> $1/L5:K start 5100 rel f; renumber $1/L5:MG start 5300 rel f; renumber $1/L5
> & ligand start 5600 rel f; renumber $1/L5:IDB start 5700 rel f; renumber
> $1/L5:HOH start 6000 rel f

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_30

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add IDB command IDB

> buttonpanel Shortcuts add paulvis command "paulvis #*"

> buttonpanel Shortcuts add paullabel command paullabel

> buttonpanel Shortcuts add paulclip command paulclip

> buttonpanel Shortcuts add paullight command paullight

> buttonpanel Shortcuts add paulsave command paulsave

> buttonpanel Shortcuts add unclip command paulunclip

> buttonpanel Shortcuts add paulambience command paulambience

> buttonpanel Shortcuts add paulstyle command paulstyle

> buttonpanel Shortcuts add delete_selected command "delete sel"

executed ChimeraX_startup_preferences_Paul_20240911.cxc  

> paulclip

Changed 216956 atom styles  
No volumes specified  

> cofron

> select /Pt:75@O3'

1 atom, 1 residue, 1 model selected  

> select add /NC:31@C

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select /NC

1718 atoms, 1898 bonds, 1 pseudobond, 96 residues, 2 models selected  

> info selection level residue

residue id /NC:26 name GLU index 0  
residue id /NC:27 name GLU index 1  
residue id /NC:28 name GLN index 2  
residue id /NC:29 name GLU index 3  
residue id /NC:30 name ASP index 4  
residue id /NC:31 name GLU index 5  
residue id /NC:8 name UNK index 6  
residue id /NC:9 name UNK index 7  
residue id /NC:10 name UNK index 8  
residue id /NC:11 name UNK index 9  
residue id /NC:12 name UNK index 10  
residue id /NC:13 name UNK index 11  
residue id /NC:14 name UNK index 12  
residue id /NC:15 name UNK index 13  
residue id /NC:16 name UNK index 14  
residue id /NC:17 name UNK index 15  
residue id /NC:18 name UNK index 16  
residue id /NC:19 name UNK index 17  
residue id /NC:20 name UNK index 18  
residue id /NC:103 name HOH  
residue id /NC:113 name HOH  
residue id /NC:1 name U index 19  
residue id /NC:2 name C index 20  
residue id /NC:3 name C index 21  
residue id /NC:4 name C index 22  
residue id /NC:5 name U index 23  
residue id /NC:6 name G index 24  
residue id /NC:7 name G index 25  
residue id /NC:8 name U index 26  
residue id /NC:9 name G index 27  
residue id /NC:10 name 2MG index 28  
residue id /NC:11 name U index 29  
residue id /NC:12 name C index 30  
residue id /NC:13 name PSU index 31  
residue id /NC:14 name A index 32  
residue id /NC:15 name G index 33  
residue id /NC:16 name U index 34  
residue id /NC:17 name G index 35  
residue id /NC:18 name G index 36  
residue id /NC:19 name U index 37  
residue id /NC:20 name H2U index 38  
residue id /NC:21 name A index 39  
residue id /NC:22 name G index 40  
residue id /NC:23 name G index 41  
residue id /NC:24 name A index 42  
residue id /NC:25 name U index 43  
residue id /NC:26 name U index 44  
residue id /NC:27 name C index 45  
residue id /NC:28 name G index 46  
residue id /NC:29 name G index 47  
residue id /NC:30 name C index 48  
residue id /NC:31 name G index 49  
residue id /NC:32 name C index 50  
residue id /NC:33 name U index 51  
residue id /NC:34 name C index 52  
residue id /NC:35 name U index 53  
residue id /NC:36 name C index 54  
residue id /NC:37 name A index 55  
residue id /NC:38 name C index 56  
residue id /NC:39 name C index 57  
residue id /NC:40 name G index 58  
residue id /NC:41 name C index 59  
residue id /NC:42 name C index 60  
residue id /NC:43 name G index 61  
residue id /NC:44 name C index 62  
residue id /NC:45 name G index 63  
residue id /NC:46 name G index 64  
residue id /NC:47 name C index 65  
residue id /NC:48 name C index 66  
residue id /NC:49 name 5MC index 67  
residue id /NC:50 name G index 68  
residue id /NC:51 name G index 69  
residue id /NC:52 name G index 70  
residue id /NC:53 name U index 71  
residue id /NC:54 name 2MU index 72  
residue id /NC:55 name PSU index 73  
residue id /NC:56 name G index 74  
residue id /NC:57 name A index 75  
residue id /NC:58 name U index 76  
residue id /NC:59 name U index 77  
residue id /NC:60 name C index 78  
residue id /NC:61 name C index 79  
residue id /NC:62 name C index 80  
residue id /NC:63 name G index 81  
residue id /NC:64 name G index 82  
residue id /NC:65 name U index 83  
residue id /NC:66 name C index 84  
residue id /NC:67 name A index 85  
residue id /NC:68 name G index 86  
residue id /NC:69 name G index 87  
residue id /NC:70 name G index 88  
residue id /NC:71 name A index 89  
residue id /NC:72 name A index 90  
residue id /NC:73 name C index 91  
residue id /NC:74 name C index 92  
residue id /NC:75 name A index 93  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: MNXA3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 23 hours, 53 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2717D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NIHPresets: 1.2.7
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
File attachment: noIDB_MYC_model_refined_060_altconf-coot.cif

noIDB_MYC_model_refined_060_altconf-coot.cif​

Attachments (1)

noIDB_MYC_model_refined_060_altconf-coot.cif​ (24.8 MB ) - added by psauer@… 5 months ago.
Added by email2trac

Change History (4)

by psauer@…, 5 months ago

Attachment: noIDB_MYC_model_refined_060_altconf-coot.cif​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 months ago

Cc: Greg Couch added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Non-chain-forming bond merges chains

...which in the 1.10 build merges the chains before the model is even shown.

comment:2 by Eric Pettersen, 5 months ago

Resolution: → fixed
Status: accepted → closed

Fixed in the next daily build. Not putting the fix into the production release because it's too late to put a change like this in the release without more real-world testing.

Fix: ​https://github.com/RBVI/ChimeraX/commit/b99acd0ded747bc889d549bfd2880b62ab73fcb1

comment:3 by psauer@…, 5 months ago 

Thank you, much appreciated!

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Wednesday, June 18, 2025 at 14:08
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Paul Sauer <psauer@interdictbio.com>
Cc: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #18017: Non-chain-forming bond merges chains
#18017: Non-chain-forming bond merges chains
-------------------------------+--------------------
          Reporter:  psauer@…  |      Owner:  pett
              Type:  defect    |     Status:  closed
          Priority:  normal    |  Milestone:
         Component:  Core      |    Version:
        Resolution:  fixed     |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------
Changes (by pett):

 * resolution:   => fixed
 * status:  accepted => closed

Comment:

 Fixed in the next daily build.  Not putting the fix into the production
 release because it's too late to put a change like this in the release
 without more real-world testing.

 Fix:
 https://github.com/RBVI/ChimeraX/commit/b99acd0ded747bc889d549bfd2880b62ab73fcb1 URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18017#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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