<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Oliver,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera doesn't handle unwrapped trajectories. You will need to use the ptraj "image" command to prevent molecules from being split across box boundaries in your final trajectory. Perhaps the other errors will not occur with the re-imaged trajectory. If not, please let me know.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Aug 19, 2009, at 4:15 AM, Koch, O (Oliver) wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Chimera Team,<br><br>I have a problem opening an AMBER trajectory using chimera v1.3 (2000/12/09). <br><br>When I look at the frames, they show this "spider web" phenomenon: Connections between atoms that should not be there. <br>Furthermore, I got errors throughout the whole file: "Error: line too long in:"<br><br>I have a topology file and a coordinate file created using leap/ptraj from the Amber Tools 1.2. <br>I could look at the files using vmd with the options "Amber 7 parm" for the topology file and "Amber coordinates with periodic box" for the coordinate file. <br>Therefore, the files should not be corrupt, but, of course, I would prefer to use Chimera for visualizing...<br><br>Can you give me any advice how to open the files correctly?<br><br>Thanks in advance.<br><br>Kind regards,<br>Oliver<br><br>Dr. Oliver Koch<br>BioChemInformatics Postdoctoral-Fellow<br>Intervet Innovation GmbH<br>Zur Propstei<br>55270 Schwabenheim, Germany<br><br>E-Mail: <span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:oliver.koch@sp.intervet.com">oliver.koch@sp.intervet.com</a><br>Phone:<span class="Apple-tab-span" style="white-space:pre"> </span>+49 (6130) 948 396<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><br>Fax:<span class="Apple-tab-span" style="white-space:pre"> </span>+49 (6130) 948 517<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><br><br>Home <span class="Apple-tab-span" style="white-space:pre"> </span>http://www.intervet.com<br><br>Sitz der Gesellschaft: Schwabenheim <span class="Apple-tab-span" style="white-space:pre"> </span> Amtsgericht Mainz, HRB 23 166<span class="Apple-tab-span" style="white-space:pre"> </span> Geschäftsführer: Dr. Peter Schmid<br><br>--------------------------------------<br>This message and any attachments are solely for the intended recipient.<br><br>If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited<br><br><br><br>-- please immediately and permanently delete.<br>--------------------------------------<br>_______________________________________________<br>Chimera-users mailing list<br>Chimera-users@cgl.ucsf.edu<br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>