<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><br><div><div>On Dec 3, 2013, at 12:28 PM, Tom Duncan <<a href="mailto:duncant@upstate.edu">duncant@upstate.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Eric, <div><br></div><div>It's not the structural info I want to extract - just the sequence alignment info.</div><div>See the remarks in the file header.</div><div><br></div><div>Thanks,</div><div>Tom<br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">-----------------------------------------------------</span></font></div><div style="margin: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Thomas M. Duncan, Ph.D.</font></div><div style="margin: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Associate Professor</font></div><div style="margin: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Dept Biochemistry & Molecular Biology</font></div><div style="margin: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">SUNY Upstate Medical University</font></div><div style="margin: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Syracuse, NY</font></div></div></span></div></span></div></span></div></span></div></span></span>
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<br><div><div>On Dec 3, 2013, at 3:00 PM, <a href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Tahoma; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Date: Tue, 3 Dec 2013 11:27:02 -0800<br>From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>To: Tom Duncan <<a href="mailto:duncant@upstate.edu">duncant@upstate.edu</a>><br>Cc: chimera-users BB <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>Subject: Re: [Chimera-users] reading PDB-format alignment files<br>Message-ID: <<a href="mailto:9EF6E8D1-3C93-4C30-AD51-2B110CF5C813@cgl.ucsf.edu">9EF6E8D1-3C93-4C30-AD51-2B110CF5C813@cgl.ucsf.edu</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>On Dec 3, 2013, at 7:47 AM, Tom Duncan <<a href="mailto:duncant@upstate.edu">duncant@upstate.edu</a>> wrote:<br><br><blockquote type="cite">Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file.<br></blockquote><br>Hi Tom,<br><span class="Apple-tab-span" style="white-space: pre; "> </span>Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket.<br><br>--Eric<br></span></blockquote></div><br></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>