id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3285 Slow graphics updates Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-05-09) Description I've run into a curious problem with the current model I'm working on (a new one, whose biggest defining feature is that it has *lots* of chains - 85, although most of them are fairly short. The model has 4713 residues in total). I suspect it's something that's gone awry with this particular session, since if I open the same model/map in a fresh ChimeraX instance it doesn't seem to happen. I *have* seen it before, though (again, on a really big model). In short, adding a new residue or deleting one triggers an *enormous* delay on the next redraw: isolde add ligand MYR ... freezes ChimeraX for well over a minute. If I then delete the residue I just added: delete sel ... and then select a random atom and go to start a simulation, that also takes forever. In the shell: from chimerax.core.commands import run %prun run(session, 'isolde sim start sel') 721612 function calls (716898 primitive calls) in 67.161 seconds Ordered by: internal time ncalls tottime percall cumtime percall filename:lineno(function) 508/406 61.573 0.121 61.683 0.152 molc.py:189(get_prop) 1 4.050 4.050 4.050 4.050 {built-in method _openmm.new_Context} 1 0.099 0.099 0.108 0.108 forcefield.py:1925(createForce) 1559 0.088 0.000 0.163 0.000 molarray.py:101(__init__) 1 0.082 0.082 0.195 0.195 forcefield.py:2030(createForce) 6 0.074 0.012 0.094 0.016 molobject.py:1606(polymers) 1 0.072 0.072 0.579 0.579 forcefield.py:1026(createSystem) 543 0.060 0.000 0.060 0.000 forcefield.py:1717(_matchImproper) 24 0.056 0.002 0.057 0.002 molc.py:202(set_prop) 1 0.053 0.053 0.108 0.108 openmm_interface.py:2670(create_openmm_topology) 406 0.052 0.000 0.052 0.000 {simtk.openmm.app.internal.compiled.matchResidueToTemplate} 131 0.045 0.000 0.046 0.000 molarray.py:656(num_selected) 135 0.026 0.000 0.026 0.000 molarray.py:300(_cpp_table_pointer) ... but when I stop that simulation and carry on, everything is back to normal. When it's in that slow state, even something as simple as `selected_residues(session)` becomes really slow (and, bizarrely, proportional to the number of residues selected). With a single residue selected: %prun selected_residues(session) 539 function calls (533 primitive calls) in 0.012 seconds Ordered by: internal time ncalls tottime percall cumtime percall filename:lineno(function) 3 0.006 0.002 0.006 0.002 molarray.py:656(num_selected) 3 0.003 0.001 0.003 0.001 molarray.py:903(num_selected) 6 0.001 0.000 0.002 0.000 molc.py:160(get_prop) 3 0.000 0.000 0.001 0.000 molc.py:189(get_prop) with all residues selected: %prun selected_residues(session) 2920449 function calls (2920443 primitive calls) in 20.521 seconds Ordered by: internal time ncalls tottime percall cumtime percall filename:lineno(function) 547446 14.452 0.000 14.452 0.000 {built-in method builtins.dir} 547446 2.613 0.000 17.064 0.000 attr_registration.py:60(get_attr) 1 1.255 1.255 20.498 20.498 structure.py:2156(selected_bonds) 1094915 1.109 0.000 1.109 0.000 {built-in method builtins.hasattr} 547446 0.964 0.000 19.137 0.000 attr_registration.py:35(_getattr_) 2 0.056 0.028 0.096 0.048 molarray.py:150() 182482 0.040 0.000 0.040 0.000 {chimerax.atomic.cymol.c_ptr_to_py_inst} Any clues? Log: > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 19 atoms, 18 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save working.cif #1 Not saving entity_poly_seq for non-authoritative sequences > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 10 atoms, 9 bonds, 1 model selected > select up 158 atoms, 159 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 19 atoms, 18 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > clipper set contourSensitivity 0.25 > clipper set contourSensitivity 0.25 > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 14 atoms, 13 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > select up 10 atoms, 9 bonds, 1 model selected > select up 158 atoms, 159 bonds, 1 model selected > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 19 atoms, 18 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > select up 48 atoms, 46 bonds, 1 model selected > select up 536 atoms, 545 bonds, 1 model selected > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > select up 19 atoms, 18 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto sel > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 24 atoms, 23 bonds, 1 model selected > select up 103 atoms, 105 bonds, 1 model selected > color sel bychain > color sel byhetero > delete sel > color sel bychain > color sel byhetero > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save working.cif #1 Not saving entity_poly_seq for non-authoritative sequences > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save working.cif #1 Not saving entity_poly_seq for non-authoritative sequences > show #!2 models > isolde restrain distances #1/C templateAtoms #2/C RMSD between 270 pruned atom pairs is 1.421 angstroms; (across all 280 pairs: 2.748) RMSD between 5 pruned atom pairs is 3.735 angstroms; (across all 10 pairs: 26.905) No further alignments of 3 or more residues found. > isolde release distances #1 > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 14 atoms, 13 bonds, 1 model selected > select up 121 atoms, 121 bonds, 1 model selected > select up 128 atoms, 127 bonds, 1 model selected > select up 188 atoms, 189 bonds, 1 model selected > select clear > select clear > show #!2 models > hide #!2 models > show #!2 models > select up 7 atoms, 6 bonds, 1 model selected > select up 434 atoms, 443 bonds, 1 model selected > hide #!2 models > show #!2 models > color #2 tan > color #2 byhetero > select clear > hide #!2 models > isolde stepto sel > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 14 atoms, 13 bonds, 1 model selected > select up 261 atoms, 264 bonds, 1 model selected > isolde stepto > isolde stepto sel > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 22 atoms, 21 bonds, 1 model selected > select up 169 atoms, 170 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > sequence chain #1/C Alignment identifier is 1.2.C > hide #!2 models > isolde stepto sel > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save working.cif #1 Not saving entity_poly_seq for non-authoritative sequences > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > show #!2 models > select #2/L:26-29 32 atoms, 34 bonds, 1 model selected > ~cartoon sel > select clear > hide #!2 models > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!3 models > hide #!3 models > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 401 atoms, 406 bonds, 1 model selected > select up 4716 atoms, 4825 bonds, 1 model selected > select down 401 atoms, 406 bonds, 1 model selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save working.cxs Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 1120, in take_snapshot from chimerax.core.state import CORE_STATE_VERSION ImportError: cannot import name 'CORE_STATE_VERSION' from 'chimerax.core.state' (/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/state.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 568, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'custom_attr_preserver' -> -> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)' RuntimeError: Error while saving session data for 'custom_attr_preserver' -> -> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)' File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 1120, in take_snapshot from chimerax.core.state import CORE_STATE_VERSION ImportError: cannot import name 'CORE_STATE_VERSION' from 'chimerax.core.state' (/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/state.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core_formats/__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 568, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'custom_attr_preserver' -> -> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)' RuntimeError: Error while saving session data for 'custom_attr_preserver' -> -> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)' File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > select up 43 atoms, 42 bonds, 1 model selected > isolde ignore ~sel ISOLDE: currently ignoring 4713 residues in model 1.2 ISOLDE: currently ignoring 4713 residues in model 3 ISOLDE: currently ignoring 3824 residues in model 2 Loading residue template for MYR from internal database > isolde ~ignore Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > delete sel > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > isolde stepto > isolde stepto > isolde stepto > select up 21 atoms, 21 bonds, 1 model selected > select up 71 atoms, 71 bonds, 1 model selected > select clear > isolde add ligand MYR > color sel bychain Profile for last activation of changes trigger: 563 function calls (526 primitive calls) in 0.001 seconds Ordered by: internal time List reduced from 95 to 20 due to restriction <20> ncalls tottime percall cumtime percall filename:lineno(function) 9/3 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py:227(__setattr__) 15 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molc.py:319(pointer) 25 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/weakref.py:567(__call__) 2 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/numpy/lib/arraysetops.py:298(_unique1d) 1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/rota_annotation.py:155(_update_graphics_if_needed) 15 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/ctypes/__init__.py:497(cast) 9 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/weakref.py:530(__init__) 9 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py:1420(remove_deleted_pointers) 6 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molc.py:189(get_prop) 1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/rama_annotation.py:191(_update_graphics_if_needed) 9 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py:101(__init__) 3 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/changes.py:165(_created_objects) 2 0.000 0.000 0.000 0.000 {built-in method builtins.sum} 15 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/numpy/core/_internal.py:251(__init__) 2 0.000 0.000 0.000 0.000 {method 'argsort' of 'numpy.ndarray' objects} 11 0.000 0.000 0.000 0.000 {built-in method numpy.empty} 1 0.000 0.000 0.001 0.001 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py:197(_activate) 68/46 0.000 0.000 0.000 0.000 {built-in method builtins.len} 10 0.000 0.000 0.001 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py:128(invoke) 15 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site- packages/numpy/core/_internal.py:268(data_as) > color sel byhetero > select up 44 atoms, 43 bonds, 1 model selected > delete sel > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select up 11 atoms, 10 bonds, 1 model selected > select up 309 atoms, 313 bonds, 1 model selected > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > close #1.2.11 > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > isolde stepto > select clear > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > isolde sim start sel > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > isolde sim start sel > isolde sim start sel > select clear > isolde add ligand MYR > color sel bychain > color sel byhetero > delete sel > isolde stepto > select /M 15002 atoms, 15173 bonds, 28 pseudobonds, 6 models selected > select #1/M 5833 atoms, 5950 bonds, 8 pseudobonds, 2 models selected > select clear > select #1/M 5833 atoms, 5950 bonds, 8 pseudobonds, 2 models selected > select clear > select clear > select #1 89287 atoms, 91241 bonds, 354 pseudobonds, 23 models selected > select clear > select clear > select #1 89287 atoms, 91241 bonds, 354 pseudobonds, 23 models selected OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 10G 40G 383M 11G 50G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia }}} " defect closed normal Performance fixed Tristan Croll Tom Goddard all ChimeraX