<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>On Sep 29, 2014, at 8:08 AM, Tony Lewis <<a href="mailto:t.lewis@ucl.ac.uk">t.lewis@ucl.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear Chimera people,<br><br><div>Many thanks to all Chimera contributors.<br><br></div><div>Please can anyone tell me if there's a way to include PDB data *inline* in Chimera script / command / Chimerax files?<br><br>PyMOL's read_pdbstr() command loads PDB data from an inline string, which means one file can contain both the structural data and the associated commands. That's rather convenient.<br><br>I would much appreciate any help on how to do the same with Chimera. Apologies if the answer is obvious.</div></div></blockquote><br></div><div>Hi Tony,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I wouldn't say the answer is obvious, but Chimera can read streams and therefore you can use a StringIO buffer to open PDB data in Chimera. Here is an example that open a histidine residue:</div><div><br></div><div><div>from StringIO import StringIO</div><div>buf = StringIO("""ATOM 1 N HIS A 1 49.668 24.248 10.436 1.00 25.00 N </div><div>ATOM 2 CA HIS A 1 50.197 25.578 10.784 1.00 16.00 C </div><div>ATOM 3 C HIS A 1 49.169 26.701 10.917 1.00 16.00 C </div><div>ATOM 4 O HIS A 1 48.241 26.524 11.749 1.00 16.00 O </div><div>ATOM 5 CB HIS A 1 51.312 26.048 9.843 1.00 16.00 C </div><div>ATOM 6 CG HIS A 1 50.958 26.068 8.340 1.00 16.00 C </div><div>ATOM 7 ND1 HIS A 1 49.636 26.144 7.860 1.00 16.00 N </div><div>ATOM 8 CD2 HIS A 1 51.797 26.043 7.286 1.00 16.00 C </div><div>ATOM 9 CE1 HIS A 1 49.691 26.152 6.454 1.00 17.00 C </div><div>ATOM 10 NE2 HIS A 1 51.046 26.090 6.098 1.00 17.00 N """)</div><div>from chimera import openModels</div><div>models = openModels.open(buf, type="PDB", identifyAs="his")</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; "><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"></span>
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