DCD "append" not working

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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.

[pett]

The direct error is fixed in the release candidate, but the coordinate sets still get replaced instead of appended, even with "replace false".

Reported by Samual Haysom.

[Tom Goddard]

Fixed.

Reading DCD coordinates with replace false was ignoring the replace false due to some optimization a few years ago to read the dcd coordinates faster.