[Chimera-users] DCD format error 1

[Eric Pettersen]

Hi again Lilian,
	Based on the files you supplied it appears that the DCD magic number  
has indeed changed (from 84 to 164) for DCDs from CHARMM v33 (and  
presumably later).  A new magic number typically indicates that the  
file format is no longer compatible with files with the old magic  
number, and that is in fact the case here.  If I change Chimera's DCD- 
reading code to just treat 164 as if it were 84, other error checks  
fail.  From my tests it also appears that VMD 1.8.7 can't read the new- 
format DCD either.
	Since the new format is undocumented AFAICT, I will be getting in  
contact with Dr. Karplus to see if I can access CHARMM's DCD-writing  
code (which isn't free) in order to add the ability to read the new  
DCDs to Chimera.  I'll keep you in the loop on that.

--Eric

On Apr 26, 2010, at 11:11 AM, Eric Pettersen wrote:

> Hi Lilian,
> 	It means that your DCD file doesn't start with the proper "magic  
> number" that all valid DCD files are supposed to contain.  Perhaps  
> if you sent me your trajectory files (directly, not via the list!) I  
> could provide more useful information.  If they are too big for  
> email, you could FTP them to one of our servers.  Let me know if you  
> need/want to do that.
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
> On Apr 23, 2010, at 1:37 AM, Lilian OLIVIERI wrote:
>
>> Hello,
>>
>> I'm having trouble using MD/Ensemble analysis tool.
>> When I try to check a MD trajectory generated by CHARMM (version  
>> C33b1), I
>> get a "DCD format error 1" message.
>>
>> Here is the Reply Log:
>>
>> MDTools 1.2 Exp (2005-08-20) by James Phillips.
>> Trajectory.DCD.MDToolsMarch97.md.help() for more info.
>> - HomoCoord 1.3 Exp (2005-08-20)
>> - Constants 1.1 Exp (2004-05-17)
>> - AtomGroup 1.4 Exp (2007-02-07)
>> - local 1.1 Exp (2004-05-17)
>> Unknown OSTYPE ??? set.  Viewing and plotting are disabled.
>> - Trans 1.2 Exp (2005-08-20)
>> - DCD 1.10 Exp (2007-02-07)
>> - Data 1.2 Exp (2005-08-20)
>> * THIS FILE IS LANGEVINEEF1.INP.
>> * USAGE, CHARMM <LANGEVINEEF1.INP >LANGEVINEEF1.OUT.
>> * RUNS LANGEVIN DYNAMICS WITH EEF1 IMPLICIT WATER.
>> *  DATE:     3/22/10     10:32:48      CREATED BY USER: lolivier
>> /labos/lbgm/lolivier/chimera/share/Trajectory/DCD/MDToolsMarch97/ 
>> md_DCD.py:121:
>> DeprecationWarning: raising a string exception is deprecated
>>  raise "DCD format error 1"
>> Traceback (most recent call last):
>>  File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/ 
>> PmwBase.py",
>> line 1747, in __call__
>>  File "CHIMERA/share/chimera/baseDialog.py", line 328, in command
>>  File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK
>>  File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply
>>  File "CHIMERA/share/Trajectory/DCD/__init__.py", line 61, in  
>> loadEnsemble
>>  File "CHIMERA/share/Trajectory/DCD/__init__.py", line 71, in  
>> loadEnsemble
>>  File "CHIMERA/share/Trajectory/DCD/DCD.py", line 35, in __init__
>>  File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line  
>> 121,
>> in __init__
>> DCD format error 1
>> DCD format error 1
>>
>>  File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line  
>> 121,
>> in __init__
>>
>> See reply log for Python traceback.
>>
>>
>> Is there a quick way to fix this problem?
>>
>> Thanks for any reply.
>>
>>
>>
>> -- 
>> Lilian Olivieri
>> PhD student
>>
>> INSERM UMR-S 665,
>> DSIMB/LBGM, Faculte des Sciences et Technologies
>> Universite de La Reunion
>> 15 Avenue René Cassin, BP 7151
>> 97715 Saint Denis Messag Cedex 09
>> La Réunion, France
>>
>> Tel: +33 262 938 227 (office)
>> Fax: +33 262 938 237
>>
>>
>> http://lbgm.univ-reunion.fr/
>> http://www.dsimb.inserm.fr/
>>
>>
>> ****************************************************************************
>> It has long been an axiom of mine that the little things are  
>> infinitely
>> the most important.
>>                             -- Sir Arthur Conan Doyle, "A Case of  
>> Identity"
>> ****************************************************************************
>>
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>
>
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