#1266 closed defect (fixed)
crosslinks and sequence viewer problems
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-08-10) Description Hi, i just tried to plot the crosslinks as network, might be that the problem is that i have different crosslinks in the same residue? thanks in advance for your support, Pascal crosslinks network pbonds Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2561, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\crosslinks\crosslinks.py", line 63, in crosslinks_network cnodes, edges = chains_and_edges(pbonds) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\crosslinks\chainplot.py", line 96, in chains_and_edges chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\crosslinks\chainplot.py", line 96, in <listcomp> chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__ return look_in_class._attr_registration.get_attr(attr_name) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'chain_id' AttributeError: 'Atom' object has no attribute 'chain_id' File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None Log: UCSF ChimeraX version: 0.8 (2018-08-10) OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation How to cite UCSF ChimeraX open "D:/UTRECHT_MS/Chimera modelling/PDB_C2S2_HL.pdb" Summary of feedback from opening D:/UTRECHT_MS/Chimera modelling/PDB_C2S2_HL.pdb --- warnings | Ignored bad PDB record found on line 207410 END Cannot find LINK/SSBOND residue TYR (24 ) Cannot find LINK/SSBOND residue GLU (65 ) Cannot find LINK/SSBOND residue VAL (119 ) Cannot find LINK/SSBOND residue GLU (139 ) Cannot find LINK/SSBOND residue GLU (180 ) 69 messages similar to the above omitted Opened PDB data containing 157892 atoms and 161044 bonds Chain information for PDB_C2S2_HL.pdb #1.2 --- Chain | Description 1.1/A 1.1/a | photosystem II protein D1 1.2/A 1.2/a | photosystem II protein D1 1.1/B 1.1/b | photosystem II CP47 reaction center protein 1.2/B 1.2/b | photosystem II CP47 reaction center protein 1.1/C 1.1/c | photosystem II CP43 reaction center protein 1.2/C 1.2/c | photosystem II CP43 reaction center protein 1.1/D 1.1/d | photosystem II D2 protein 1.2/D 1.2/d | photosystem II D2 protein 1.1/E 1.1/e | PSII reaction center subunit V 1.2/E 1.2/e | PSII reaction center subunit V 1.1/F 1.1/f | cytochrome B559 subunit β, PSBF 1.2/F 1.2/f | cytochrome B559 subunit β, PSBF 1.1/G 1.1/N 1.1/Y 1.1/g 1.1/n 1.1/y | lhcii TYPE I CAB-8 1.2/G 1.2/N 1.2/Y 1.2/g 1.2/n 1.2/y | lhcii TYPE I CAB-8 1.1/H 1.1/h | photosystem II reaction center protein H 1.2/H 1.2/h | photosystem II reaction center protein H 1.1/I 1.1/i | photosystem II reaction center protein I, PSBI 1.2/I 1.2/i | photosystem II reaction center protein I, PSBI 1.1/J 1.1/j | PSII-J 1.2/J 1.2/j | PSII-J 1.1/K 1.1/k | PSII-K 1.2/K 1.2/k | PSII-K 1.1/L 1.1/l | PSII-L 1.2/L 1.2/l | PSII-L 1.1/M 1.1/m | PSII-M 1.2/M 1.2/m | PSII-M 1.1/O 1.2/O 1.1/o 1.2/o | oxygen-evolving enhancer protein 1, chloroplastic 1.1/P 1.2/P 1.1/p 1.2/p | oxygen-evolving enhancer protein 2, chloroplastic 1.1/Q 1.1/q | oxygen-evolving enhancer protein 3 1.2/Q 1.2/q | oxygen-evolving enhancer protein 3 1.1/R 1.1/r | light harvesting chlorophyll A/B-binding protein LHCB4, CP29 1.2/R 1.2/r | light harvesting chlorophyll A/B-binding protein LHCB4, CP29 1.1/S 1.1/s | light harvesting chlorophyll A/B-binding protein LHCB5, CP26 1.2/S 1.2/s | light harvesting chlorophyll A/B-binding protein LHCB5, CP26 1.1/T 1.1/t | PSII-T 1.2/T 1.2/t | PSII-T 1.1/W 1.2/W 1.1/w 1.2/w | photosystem II reaction center protein W 1.1/X 1.1/x | photosystem II reaction center protein X 1.2/X 1.2/x | photosystem II reaction center protein X 1.1/Z 1.2/Z 1.1/z 1.2/z | PSII-Z set bgColor gray hide selAtoms surfaces hide selAtoms surfaces hide selAtoms show selAtoms ribbons distance #1.1/R:177@CA #1.1/R:170@CA radius 0.5 dashes 12 color gold Distance between PDB_C2S2_HL.pdb #1.1/R LYS 177 CA and LYS 170 CA: 12.850Å crosslinks #1.1/R:177@CA #1.1/R:170@CA radius 0.5 dashes 12 color gold sequence chain #1.1/R Alignment identifier is 1.1.R sequence chain #1.2/R Alignment identifier is 1.2.R invert selR Unknown command: invert selR invert sel Unknown command: invert sel help help:user didn't expected commands hrefs to be to tools/sequenceviewer.html on line 239 select up 243 atoms, 248 bonds, 1 model selected select up 2805 atoms, 2887 bonds, 1 model selected select ~ sel 155087 atoms, 158157 bonds, 2098 pseudobonds, 5 models selected select color tan tranparency 0.5 Expected an objects specifier or a keyword help help:quickstart help help:quickstart help help:user select color tan tranparency 50 Expected an objects specifier or a keyword select color tan tranparency 50 target c Expected an objects specifier or a keyword select color tan Expected an objects specifier or a keyword select color tan all Expected an objects specifier or a keyword color sel tan tranparency sel 50 target c Unknown command: tranparency sel 50 target c tranparency sel 0.5 target c Unknown command: tranparency sel 0.5 target c transparency sel 0.5 target c transparency sel 50 target c sequence chain #1.1/r Alignment identifier is 1.1.r color #1.1/r #1.2/r #1.1/R #1.2/R green select up 157892 atoms, 161044 bonds, 2168 pseudobonds, 5 models selected select up 157892 atoms, 161044 bonds, 2168 pseudobonds, 5 models selected transparency sel 70 target c transparency #1.1/r #1.2/r #1.1/R #1.2/R 0 target c save session "D:/UTRECHT_MS/Chimera modelling/Lhcb4_INTRALINKS.cxs" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\region_browser.py", line 438, in <lambda> lambda e, s=self: s._mouse_up_cb(e, double=True) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\region_browser.py", line 1538, in _mouse_up_cb self.enter() AttributeError: 'RegionBrowser' object has no attribute 'enter' AttributeError: 'RegionBrowser' object has no attribute 'enter' File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\region_browser.py", line 1538, in _mouse_up_cb self.enter() See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. help help:devel distance #1.1/R:191@CA #1.1/R:170@CA radius 0.5 dashes 12 color gold Distance between PDB_C2S2_HL.pdb #1.1/R LYS 191 CA and LYS 170 CA: 13.441Å distance #1.1/R:191@CA #1.2/R:170@CA radius 0.5 dashes 12 color red Distance between PDB_C2S2_HL.pdb #1.1/R LYS 191 CA and PDB_C2S2_HL.pdb #1.2/R LYS 170 CA: 92.788Å distance #1.1/R:177@CA #1.1/R:170@CA radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1.1/R:177@CA #1.2/R:170@CA radius 0.5 dashes 12 color red Distance between PDB_C2S2_HL.pdb #1.1/R LYS 177 CA and PDB_C2S2_HL.pdb #1.2/R LYS 170 CA: 81.762Å distance #1.1/R:190@CA #1.1/R:200@CA radius 0.5 dashes 12 color gold Distance between PDB_C2S2_HL.pdb #1.1/R LYS 190 CA and LYS 200 CA: 14.934Å distance #1.1/R:190@CA #1.2/R:200@CA radius 0.5 dashes 12 color red Distance between PDB_C2S2_HL.pdb #1.1/R LYS 190 CA and PDB_C2S2_HL.pdb #1.2/R LYS 200 CA: 115.008Å distance #1.1/R:190@CA #1.1/R:200@CA radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' save session "D:/UTRECHT_MS/Chimera modelling/Lhcb4_INTRALINKS.cxs" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. save session "D:/UTRECHT_MS/Chimera modelling/Lhcb4_INTRALINKS.cxs" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. distance #1.1/C:339@CA distance #1.1/:228@CA radius 0.5 dashes color gold Missing or invalid "atoms" argument: Expected two atoms to be specified (1 specified) distance #1.1/C:339@CA distance #1.1/:228@CA radius 0.5 dashes color gold Missing or invalid "atoms" argument: Expected two atoms to be specified (1 specified) distance #1.1/C:339@CA distance #1.1/:228@CA radius 0.5 dashes color gold Missing or invalid "atoms" argument: Expected two atoms to be specified (1 specified) [deleted many "distance" commands] Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:228@CA #1.2/:44@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:8@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:405@CA #1.2/:186@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/c:339@CA #1.2/:364@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: Expected two atoms to be specified (1 specified) distance #1.2/:56@CA #1.2/:127@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: only initial part "#1.2" of atom specifier valid distance #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "atoms" argument: Expected two atoms to be specified (1 specified) crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:145@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:118@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:183@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/S:46@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:26@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:274@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:192@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:26@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:41@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:183@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:68@CA #1.2/:42@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:26@CA #1.2/:274@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/B:349@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:228@CA #1.2/:67@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:457@CA #1.2/:387@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:172@CA #1.2/:147@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:27@CA #1.2/:438@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:111@CA #1.2/:99@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:239@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:27@CA #1.2/:438@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/B:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:239@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/S:46@CA #1.2/S:39@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:172@CA #1.2/:147@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:111@CA #1.2/:99@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:247@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/S:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:441@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:192@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:481@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/S:44@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:182@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:441@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:382@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:244@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/C:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:228@CA #1.2/B:349@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:186@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:117@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:54@CA #1.2/:265@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:69@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:41@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:28@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:253@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:247@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:45@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:45@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/C:339@CA #1.2/:555@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:182@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:16@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:228@CA #1.2/:44@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:405@CA #1.2/:186@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:364@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:56@CA #1.2/:127@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/C:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:145@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:118@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:183@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:41@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/s:46@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:26@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:274@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:27@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:192@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:26@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:41@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:183@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:68@CA #1.2/:42@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:217@CA #1.2/:225@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:26@CA #1.2/:274@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:382@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/b:349@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:228@CA #1.2/:67@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:457@CA #1.2/:387@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:172@CA #1.2/:147@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:27@CA #1.2/:438@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:111@CA #1.2/:99@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:239@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:27@CA #1.2/:438@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/b:349@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:239@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/s:46@CA #1.2/s:39@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:172@CA #1.2/:147@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:111@CA #1.2/:99@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:247@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/s:46@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:441@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:192@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:481@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/s:44@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:41@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:182@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:9@CA #1.2/:79@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:145@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:441@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:382@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:169@CA #1.2/:162@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:244@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:216@CA #1.2/:239@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/c:381@CA radius 0.5 dashes 20 color gold crosslinks #1.2/:228@CA #1.2/b:349@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:186@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:117@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:212@CA #1.2/:205@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:169@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:54@CA #1.2/:265@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:8@CA #1.2/:85@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:77@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:69@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:41@CA #1.2/:242@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:42@CA #1.2/:28@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:182@CA #1.2/:253@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:247@CA #1.2/:243@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:90@CA #1.2/:230@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:45@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:26@CA #1.2/:45@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/c:339@CA #1.2/:228@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/c:339@CA #1.2/:555@CA radius 0.5 dashes 20 color gold Expected a keyword crosslinks #1.2/:42@CA #1.2/:182@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:16@CA #1.2/:35@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:27@CA #1.2/:22@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:228@CA #1.2/:44@CA radius 0.5 dashes 20 color gold Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid crosslinks #1.2/:83@CA #1.2/:306@CA radius 0.5 das Missing or invalid "pbonds" argument: only initial part "#1.2" of atom specifier valid help help:user crosslinks histogram Missing or invalid "pbonds" argument: empty atom specifier crosslinks network pbonds Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py", line 205, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2561, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\crosslinks.py", line 63, in crosslinks_network cnodes, edges = chains_and_edges(pbonds) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\chainplot.py", line 96, in chains_and_edges chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\chainplot.py", line 96, in <listcomp> chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__ return look_in_class._attr_registration.get_attr(attr_name) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'chain_id' AttributeError: 'Atom' object has no attribute 'chain_id' File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. crosslinks histogram pbonds crosslinks network pbonds Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py", line 205, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2561, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\crosslinks.py", line 63, in crosslinks_network cnodes, edges = chains_and_edges(pbonds) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\chainplot.py", line 96, in chains_and_edges chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\crosslinks\chainplot.py", line 96, in <listcomp> chains = [(a.structure, a.chain_id) for a in pb.atoms] File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__ return look_in_class._attr_registration.get_attr(attr_name) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'chain_id' AttributeError: 'Atom' object has no attribute 'chain_id' File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 66, in get_attr raise AttributeError("'%s' object has no attribute '%s'" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (5)
comment:1 by , 7 years ago
Component: | Unassigned → Structure Analysis |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → crosslinks and sequence viewer problems |
comment:2 by , 7 years ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
follow-up: 3 comment:3 by , 7 years ago
Awesome, thanks! Il giorno gio 23 ago 2018 alle ore 22:16 ChimeraX < ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:
follow-up: 4 comment:4 by , 7 years ago
Hi Eric, sorry for writing you again but the daily build do not lunch on my PC, i tried to install it twice actually but it doesn't work. I also had this problem randomly with the daily builds, some days is working, some day not. Bests, P Il giorno gio 23 ago 2018 alle ore 23:28 Pascal Albanese < pascal.albanese@polito.it> ha scritto:
comment:5 by , 7 years ago
I am able to run the current daily build both on my mac and on a Windows 10 machine in my lab. What does "doesn't work" mean exactly? Do you get any error messages?
--Eric
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Hi Pascal,
--Eric