Opened 9 years ago
Closed 9 years ago
#431 closed defect (fixed)
Error opening PDB with blank chain id
| Reported by: | Tom Goddard | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
open input_nowater.pdb
Summary of problems opening input_nowater.pdb:
Warnings:
Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Opened PDB data containing 582 atoms and 589 bonds
Model 1 (input_nowater.pdb) has no secondary structure assignments. Running dssp using default settings.
Traceback (most recent call last):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 146, in execute
cmd.run(cmd_text)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2206, in run
results.append(ci.function(session, kw_args))
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 97, in open
models = session.models.open(paths, format=format, name=name, kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 342, in open
self.add(models)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 231, in add
m.added_to_session(session)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/structure.py", line 1420, in added_to_session
super().added_to_session(session)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/structure.py", line 112, in added_to_session
if self.num_chains == 0:
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molc.py", line 37, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Chain ID "(blank)" too long, maximum 4 characters.
Attachments (1)
Change History (3)
by , 9 years ago
| Attachment: | input_nowater.pdb added |
|---|
comment:1 by , 9 years ago
| Status: | new → accepted |
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comment:2 by , 9 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |