Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2924 closed defect (fixed)

Attempt to link markers in different models

Reported by: rohou.alexis@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-20)
Description
I was just playing around with "marker link", created two markers, models  #1001 and #1002. The first one was created by the "measure center" command. The second one was created by "marker", with an atom-spec.

Log:
Startup Messages  
---  
warnings | 'clip' is a prefix of an existing command 'clipper'  
Populating font family aliases took 4185 ms. Replace uses of missing font
family "Lucida Sans" with one that exists to avoid this cost.  
note | Updating list of available bundles failed: [Errno 8] nodename nor
servname provided, or not known  
  
UCSF ChimeraX version: 0.92 (2020-02-20)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif  
---  
warnings | Unknown polymer entity '1' near line 139  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif  
---  
warnings | Unknown polymer entity '1' near line 139  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #3  
---  
Chain | Description  
A B C D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 360 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

Tried to create model #10 which already exists  

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde2.cif  
---  
warnings | Unknown polymer entity '1' near line 139  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for model  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C 1.1/D | ?  
  
Done loading forcefield  

QWidget::repaint: Recursive repaint detected  

> view /A:469

> volume #1.2.1.1 level 0.2169

> select /A:469

7 atoms, 6 bonds, 1 model selected  

> select clear

reverting to start  

> select /A:948

16 atoms, 15 bonds, 1 model selected  

> view /A:948

> select clear

> select clear

reverting to start  

Unknown command: LA:948  

> view /L

> view /M

> select up

45 atoms, 47 bonds, 1 model selected  

> view /L

> select /L

45 atoms, 47 bonds, 1 model selected  

> help hbon

> hbonds #1.1

2145 hydrogen bonds found  

> view /M

> view /L

> view /M

> select up

45 atoms, 47 bonds, 1 model selected  

> ~hbonds

> view /L

> view /M

> view /L

> volume #1.2.1.1 level 0.1687

> volume #1.2.1.1 level 0.1205

> volume #1.2.1.1 level 0.2295

> view /M

> select clear

> hbonds #1.1

2145 hydrogen bonds found  

> select clear

> ~hbonds

> select /O

45 atoms, 47 bonds, 1 model selected  

> select up

45 atoms, 47 bonds, 1 model selected  

> view /L

> view /M

> view /N

Expected an objects specifier or a view name or a keyword  

> view /O

> view /L

> view /M

> view /O

> select /O

45 atoms, 47 bonds, 1 model selected  

> save
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde3.cif
> format mmcif models #1.1

Not saving entity_poly_seq for non-authoritative sequences  

> save
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde3.pdb
> format pdb models #1.1

> view /L

> select /L

45 atoms, 47 bonds, 1 model selected  

> view /M

> view /N

> select /N

45 atoms, 47 bonds, 1 model selected  

> view /O

> select up

36368 atoms, 36764 bonds, 1 model selected  

> select up

36368 atoms, 36764 bonds, 3 models selected  

> select clear

> save
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif
> format mmcif models #1.1

Not saving entity_poly_seq for non-authoritative sequences  

> save
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.pdb
> format pdb models #1.1

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe.pdb

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe.pdb  
---  
warnings | Ignored bad PDB record found on line 3  
HELIX 1 1 PRO A 449 SER A 455 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 4  
HELIX 2 2 ILE A 459 LEU A 465 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 5  
HELIX 3 3 PRO A 485 ASN A 492 1 Generated by MOE 8  
  
Ignored bad PDB record found on line 6  
HELIX 4 4 ASP A 495 LYS A 504 1 Generated by MOE 10  
  
Ignored bad PDB record found on line 7  
HELIX 5 5 ALA A 517 GLY A 524 1 Generated by MOE 8  
  
146 messages similar to the above omitted  
  
Chain information for 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> view /L

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif  
---  
warnings | Unknown polymer entity '1' near line 140  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  
Chain information for model  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C 1.1/D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> view /L

> hbonds #1.1

2150 hydrogen bonds found  

> view /M

> view /N

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif  
---  
warnings | Unknown polymer entity '1' near line 140  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  
Chain information for model  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C 1.1/D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif  
---  
warnings | Unknown polymer entity '1' near line 140  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2.pdb

Chain information for 6pqq_S448-T1078_ali_lig_trim2.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker model, chain A (#1) with 6pqq_S448-T1078_ali_lig_trim2.pdb, chain A
(#3), sequence alignment score = 2876.6  
RMSD between 556 pruned atom pairs is 0.933 angstroms; (across all 562 pairs:
0.958)  
  

> view orient

> view /L

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif  
---  
warnings | Unknown polymer entity '1' near line 137  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 6pqq_S448-T1078_ali.cif #4  
---  
Chain | Description  
A B C D | ?  
  

> hide #!3 models

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4.cif  
---  
warnings | Unknown polymer entity '1' near line 140  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Unable to fetch template for 'LXY': might be missing bonds  
Atom H1 is not in the residue template for SER #448 in chain A  
Atom H1 is not in the residue template for SER #448 in chain B  
Atom H1 is not in the residue template for SER #448 in chain C  
Atom H1 is not in the residue template for SER #448 in chain D  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain L  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain M  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain O  
Unable to fetch template for 'LXY': might be missing bonds  
Missing or invalid residue template for LXY #1 in chain N  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | ?  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif  
---  
warnings | Unknown polymer entity '1' near line 137  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 6pqq_S448-T1078_ali.cif #3  
---  
Chain | Description  
A B C D | ?  
  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.cif
> name model

File not found:
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.cif  

> close

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 800 800

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.pdb
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.pdb  
---  
warnings | Ignored bad PDB record found on line 3  
HELIX 1 1 PRO A 449 SER A 455 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 4  
HELIX 2 2 ILE A 459 LEU A 465 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 5  
HELIX 3 3 PRO A 485 ASN A 492 1 Generated by MOE 8  
  
Ignored bad PDB record found on line 6  
HELIX 4 4 ASP A 495 LYS A 504 1 Generated by MOE 10  
  
Ignored bad PDB record found on line 7  
HELIX 5 5 ALA A 517 GLY A 524 1 Generated by MOE 8  
  
148 messages similar to the above omitted  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc
> name map

Opened volume_72_2_sharp_8_2p99_m90_0_20_fom_resample.mrc, grid size
324,324,324, pixel 1, shown at level 0.0808, step 2, values float32  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif  
---  
warnings | Unknown polymer entity '1' near line 137  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 6pqq_S448-T1078_ali.cif #3  
---  
Chain | Description  
A B C D | ?  
  

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1/A rgb(212,130,97)

> color #1/B rgb(137,187,206)

> color #1/C rgb(248,238,166)

> color #1/D rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.2 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> hide #!3 models

> view /M

> view /L

> view /L

> select zone /L 4.5 extend true residues true

Selected 714 atoms, 3 surfaces  

> show sel

> ~show HC

> color sel byhetero

> ~select

Nothing selected  

> help pseudo

No help found for 'pseudo'  

> select zone /L 4.5 extend true residues true

Selected 714 atoms, 3 surfaces  

> show sel

> ~show HC

> select clear

> help measure center

> measure center #1/A:841@CD1,CE1,CZ,CE2,CD2,CG

Center of mass of 6 atoms = (142.89, 142.20, 192.00)  

> measure center #1/A:841@CD1,CE1,CZ,CE2,CD2,CG mark true

Center of mass of 6 atoms = (142.89, 142.20, 192.00)  

> close #4

> measure center #1/A:841@CD1,CE1,CZ,CE2,CD2,CG mark true modelId 1001

Center of mass of 6 atoms = (142.89, 142.20, 192.00)  

> close #1001

> measure center #1/A:841@CD1,CE1,CZ,CE2,CD2,CG mark true radius 0.1 modelId
> 1001

Center of mass of 6 atoms = (142.89, 142.20, 192.00)  

> help pseud

No help found for 'pseud'  

> help marker

Missing or invalid "position" argument: Expected 3 floats or object specifier  

Missing or invalid "position" argument: Expected 3 floats or object specifier  

Missing or invalid "position" argument: Expected 3 floats or object specifier  

> select #1/A:840@CD2

1 atom, 1 model selected  

> select #1001/M:1@M

1 atom, 1 model selected  

Missing or invalid "position" argument: Expected 3 floats or object specifier  

> select #1/A:840@CD2

1 atom, 1 model selected  

> marker #1002 #1/A:840@CD2

> marker link #1001 #1002

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmd.py", line 81, in marker_link  
link = create_link(m1, m2, rgba, radius)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/markers.py", line 44, in create_link  
b = m.new_bond(atom1,atom2)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1542, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
TypeError: Cannot bond atoms in different molecules  
  
TypeError: Cannot bond atoms in different molecules  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1542, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.

Change History (5)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Attempt to link markers in different models

At a minimum, the error should be caught and a better error message presented to the user (or the attempted cross-model link detected beforehand). Perhaps something even better/smarter could be done.

Also, at the top of the log note the alarming amount of time it took to populate font families: 4185ms!

comment:2 by Eric Pettersen, 6 years ago

Cc: Eric Pettersen added

in reply to:  3 ; comment:3 by goddard@…, 6 years ago 

Marker links are bonds which can only be between atoms of the same model.  I will make it give a clear error message.

Both measure center and the marker command allow specifying model id number so you can make those markers part of the same model.

The long time at startup populating font families is a problem introduced by Qt 5.14.  We have backed down to Qt 5.12 due to other problems so current daily builds do not have that problem.

comment:4 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Made better error message with no traceback.

Markers could be enhanced to use pseudobonds as links which could go between models but this would increase the complexity of the code and decrease the performance. Would need a strong case why this is useful.

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

Thank you! I don't see a strong unmet need as is.

On Mon, Mar 9, 2020 at 10:34 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
Note: See TracTickets for help on using tickets.