<div dir="ltr"><div><div><div>Hi Eric:<br></div>I tried with my files. Thanks a lot for allowing NAMD users to catch segname segments with CHIMERA<br><br></div>all the best<br><br></div>francesco<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 1, 2015 at 8:12 PM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hmm, Chimera was being a bit of stickler in that it wasn't reading the columns that included the segment ID unless the ATOM records had a full 80 characters. The ATOM records in your file are a little shorter (78 characters). I have modified the Chimera code to be a little more flexible in that regard. If you get tonight's daily build, it will process the segment IDs in your file. Look for builds dated April 1 or later.<div><div><br></div><div>--Eric</div><div><br><div><div><div class="h5"><div>On Apr 1, 2015, at 8:27 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr"><div><div><div>Hi Eric:<br></div>If I did correctly, it does not work.<br><br></div>Attached is a pdb file from work that I recently published. If relevant, I could also provide psf/dcd. In fact, my main interest is in describing the MD trajectory with chimera/centroid, while highlighting in different colors the various chains and residues of particular interest<br><br></div><div>Thanks a lot for your interest<br><br></div><div>francesco<br></div><div><br></div>define centroid <br><div><br><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Mar 30, 2015 at 11:32 PM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Francesco,<div><span style="white-space:pre-wrap"> </span>It should be available as the atom attribute pdbSegment, <i>e.g.</i> "color red @/pdbSegment=XY2". If that doesn't work, please let me know and attach a PDB file with segment info in it that I can use for testing.<div><br></div><div>--Eric</div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu/" target="_blank">http://www.cgl.ucsf.edu</a><br><br><div><div><div><div>On Mar 28, 2015, at 6:34 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div><div dir="ltr"><div>Hello:<br><br></div><div>May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes)<br><br></div><div>Thanks<br></div><div>francesco pietra<br></div></div></div></div>
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