<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Lilian,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><br></div><div>--Eric<br><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div><div><div>On Apr 23, 2010, at 1:37 AM, Lilian OLIVIERI wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>I'm having trouble using MD/Ensemble analysis tool.<br>When I try to check a MD trajectory generated by CHARMM (version C33b1), I<br>get a "DCD format error 1" message.<br><br>Here is the Reply Log:<br><br>MDTools 1.2 Exp (2005-08-20) by James Phillips. <br>Trajectory.DCD.MDToolsMarch97.md.help() for more info.<br>- HomoCoord 1.3 Exp (2005-08-20)<br>- Constants 1.1 Exp (2004-05-17)<br>- AtomGroup 1.4 Exp (2007-02-07)<br>- local 1.1 Exp (2004-05-17)<br>Unknown OSTYPE ??? set. Viewing and plotting are disabled.<br>- Trans 1.2 Exp (2005-08-20)<br>- DCD 1.10 Exp (2007-02-07)<br>- Data 1.2 Exp (2005-08-20)<br>* THIS FILE IS LANGEVINEEF1.INP.<br>* USAGE, CHARMM <LANGEVINEEF1.INP >LANGEVINEEF1.OUT.<br>* RUNS LANGEVIN DYNAMICS WITH EEF1 IMPLICIT WATER.<br>* DATE: 3/22/10 10:32:48 CREATED BY USER: lolivier<br>/labos/lbgm/lolivier/chimera/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py:121:<br>DeprecationWarning: raising a string exception is deprecated<br> raise "DCD format error 1"<br>Traceback (most recent call last):<br> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",<br>line 1747, in __call__<br> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command<br> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK<br> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply<br> File "CHIMERA/share/Trajectory/DCD/__init__.py", line 61, in loadEnsemble<br> File "CHIMERA/share/Trajectory/DCD/__init__.py", line 71, in loadEnsemble<br> File "CHIMERA/share/Trajectory/DCD/DCD.py", line 35, in __init__<br> File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121,<br>in __init__<br>DCD format error 1<br>DCD format error 1<br><br> File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121,<br>in __init__<br><br>See reply log for Python traceback.<br><br><br>Is there a quick way to fix this problem?<br><br>Thanks for any reply.<br><br><br><br>-- <br>Lilian Olivieri<br>PhD student<br><br>INSERM UMR-S 665,<br>DSIMB/LBGM, Faculte des Sciences et Technologies<br>Universite de La Reunion<br>15 Avenue René Cassin, BP 7151<br>97715 Saint Denis Messag Cedex 09<br>La Réunion, France<br><br>Tel: +33 262 938 227 (office)<br>Fax: +33 262 938 237<br><br><br><a href="http://lbgm.univ-reunion.fr/">http://lbgm.univ-reunion.fr/</a><br>http://www.dsimb.inserm.fr/<br><br><br>****************************************************************************<br>It has long been an axiom of mine that the little things are infinitely<br>the most important.<br> -- Sir Arthur Conan Doyle, "A Case of Identity"<br>****************************************************************************<br><br>_______________________________________________<br>Chimera-users mailing list<br>Chimera-users@cgl.ucsf.edu<br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br><br></div></blockquote></div><br></div><br></body></html>