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)

input_nowater.pdb (38.3 KB ) - added by Tom Goddard 9 years ago.

Download all attachments as: .zip

Change History (3)

by Tom Goddard, 9 years ago

Attachment: input_nowater.pdb added

comment:1 by Eric Pettersen, 9 years ago

Status: newaccepted

comment:2 by Eric Pettersen, 9 years ago

Resolution: fixed
Status: acceptedclosed
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