Reading DCD: UnicodeDecodeError: unexpected end of data

[girl_toon@…]

Hi

How to handle this error?

UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc3 in position 0: unexpected end of data

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\md_crds\dcd\MDToolsMarch97\md_DCD.py", line 175, in
dat = [c.decode('utf-8') for c in up('80c',f.read(cs('80c')))]

See log for complete Python traceback.

          Thanks

[pett]

Hi,

The error seems to indicate that your DCD file is truncated. Does the file work in other applications, such as regular Chimera or VMD?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[girl_toon@…]

The DCD file was very big, so I cut few frames using catdcd, but it opened with VMD.

#1607: Reading DCD: UnicodeDecodeError: unexpected end of data
-------------------------------------------+----------------------
          Reporter:  girl_toon@…           |      Owner:  pett
              Type:  defect                |     Status:  feedback
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi,
         The error seems to indicate that your DCD file is truncated.  Does
 the file work in other applications, such as regular Chimera or VMD?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab


--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1607#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

None of the DCD files I have access to exhibit this problem. Is there any chance you could use catDCD to produce a small DCD file and, assuming it still produces this error, send it and the associated structure file so that I can investigate further?

--Eric