id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2924 Attempt to link markers in different models rohou.alexis@… Tom Goddard "{{{ 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. }}} " defect closed normal Volume Data fixed Eric Pettersen all ChimeraX