Thanks, Elaine and Eric. That works. <br><br>Mingfeng<br><br><div><span class="gmail_quote">On 2/5/07, <b class="gmail_sendername">Eric Pettersen</b> <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">Hi Mingfeng,<div><span><span style="white-space: pre;"> </span>Chimera's original PDB-parsing code was quite strict for exact format adherence. Over time, I have made it more forgiving in many ways, but right now you're getting caught by one of it's remaining strictures: according to the PDB format spec, the model number of a MODEL record has to be in columns 11-14. In your example the model numbers start in column 7. This problem will be fixed in the next snapshot, which we will be working on putting out next week.
</span></div><div><span><span style="white-space: pre;"> </span>Also, as Elaine pointed out, you need to use ENDMDL records instead of END records.</span></div><div><br></div><div><span>--Eric</span></div><div><span><br><div>
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<span> </span>Eric Pettersen</font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5">
<span> </span>UCSF Computer Graphics Lab</font></p> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5">
<span> </span><a href="mailto:pett@cgl.ucsf.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">pett@cgl.ucsf.edu</a></font></p><span class="q"> <p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5">
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<div>On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:</div><br></span><blockquote type="cite"><div><span class="e" id="q_1109331051f16853_5">Dear Chimera users and developers,<br><br>I'd like to use chimera to view the motions of a protein. If all the snapshots are to be saved in a single PDB file, what's the correct format for them?
<br><br>I tried the following, but chimera complained that a single structure is included only. <br><br>Thanks,<br>Mingfeng<br>------------------<br>MODEL 1<br>ATOM 1 N ALA 1 -4.564 -7.956 -6.531 1.00
0.00 N<br>ATOM 2 CA ALA 1 -5.237 -8.746 -5.532 1.00 0.00 C <br>ATOM 3 C ALA 1 -4.360 -9.172 -4.378 1.00 0.00 C<br>...<br>ATOM 81 HN ALA 10
0.195 11.398 3.736 1.00 0.00 H<br>END<br>MODEL 2<br>ATOM 1 N ALA 1 - 5.031 -8.234 -5.174 1.00 0.00 N<br>....<br> END<br></span></div><span class="q"><div style="margin: 0px;">
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