id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3252 "DCD ""append"" not working" bssfh@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description I want to load a series of trajectories, stored as .dcd files, into a pdb file. When I use the replace false option whilst opening the trajectory, I get a python error. When I use the default or specify replace true, the command works but it overwrites the previous trajectory Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" Must specify a structure model to read the coordinates into Missing or invalid ""filename"" argument: Expected a file name > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb"" Summary of feedback from opening /Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic Biology (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb --- warning | Ignored bad PDB record found on line 1 REMARK original generated coordinate pdb file Chain information for LL_cMDFF_model4_autopsf.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide atoms > show cartoons > lighting simple > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 102 new frames Missing or invalid ""models"" argument: empty atom specifier > mseries #1 > mseries slider #1 > movie record > movie encode /Users/samuelhaysom/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/samuelhaysom/Desktop/movie.mp4 > mseries slider #1 step 1 > mseries slider #1 step 1 Expected a keyword > coordset slider #1 > close session > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb"" Summary of feedback from opening /Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic Biology (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb --- warning | Ignored bad PDB record found on line 1 REMARK original generated coordinate pdb file Chain information for LL_cMDFF_model4_autopsf.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 102 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth5_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth4_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth3_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth2_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth1_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth0_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > coordset slider #1 > close session > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb"" Summary of feedback from opening /Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic Biology (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb --- warning | Ignored bad PDB record found on line 1 REMARK original generated coordinate pdb file Chain information for LL_cMDFF_model4_autopsf.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 replace false Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 729, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 507, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 460, in open_data models, status = open_func(*args, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) NameError: name 'model' is not defined NameError: name 'model' is not defined File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) See log for complete Python traceback. > coordset slider #1 > hide cartoons > hide atoms > show cartoons > close session > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb"" Summary of feedback from opening /Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic Biology (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/model4/LL_cMDFF_model4_autopsf.pdb --- warning | Ignored bad PDB record found on line 1 REMARK original generated coordinate pdb file Chain information for LL_cMDFF_model4_autopsf.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide cartoons > hide atoms > show cartoons > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 replace false Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 729, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 507, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 460, in open_data models, status = open_func(*args, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) NameError: name 'model' is not defined NameError: name 'model' is not defined File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) See log for complete Python traceback. > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 102 new frames Missing ""replace"" keyword's argument > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 replace false Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 729, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 507, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 460, in open_data models, status = open_func(*args, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) NameError: name 'model' is not defined NameError: name 'model' is not defined File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) See log for complete Python traceback. > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth6_gscale1.dcd"" > structureModel #1 replace false Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 729, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 507, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 460, in open_data models, status = open_func(*args, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) NameError: name 'model' is not defined NameError: name 'model' is not defined File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) See log for complete Python traceback. Missing ""replace"" keyword's argument Missing ""replace"" keyword's argument > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth5_gscale1.dcd"" > structureModel #1 replace true Replaced existing frames of LL_cMDFF_model4_autopsf.pdb #1 with 100 new frames > open ""/Users/samuelhaysom/OneDrive - University of Leeds/PhD Mechanistic > Biology > (2018-22)/Computing/MDFF/200428_cMDFF_LL_OO/Run4_model4/Replicate_3/map_smooth5_gscale1.dcd"" > structureModel #1 replace false Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 729, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 507, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 460, in open_data models, status = open_func(*args, **kw) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) NameError: name 'model' is not defined NameError: name 'model' is not defined File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/md_crds/__init__.py"", line 30, in open_file return [], ""Added %d frames to %s"" % (num_coords, model) See log for complete Python traceback. > mseries slider #1 Unknown command: trajectory OpenGL version: 4.1 ATI-2.11.21 OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal MD/Ensemble Analysis fixed Eric Pettersen all ChimeraX