<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 11, 2011, at 4:20 PM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> Hi Mike,<br> <br> I see your test file contains Cu1 and Chimera shows that in a label as CU1 with all upper case. That surprises me. Our expert on that Eric Pettersen can explain it next week. You may be right that Chimera knows the atomic elements and could selectively capitalize labels according to your preferences when the atom name matches the element symbol. Again it is something Eric can advise on.</div></blockquote><br></div><div>The upper-casing has been there since "time immemorial" (i.e. Greg doesn't remember why he wrote the code that way ;-) ). I could take it out in the 1.6 daily build and see what happens. It would only affect non-standard PDB files, since all RCSB PDB files use upper case exclusively. The possible negative consequence would be that if some program generates PDB files where the backbone atoms are "ca", "n", "c", etc. then Chimera would no longer recognize them as backbone and would not depict them with ribbons, would not automatically get their atom types correct, etc.</div><div><br></div><div>Are there major programs out there that generate lower case atom names? Beats me. I can't think of any off the top of my head. If anyone can, please chime in! I guess I'll remove the upper casing (in the 1.6 build) if no one does...</div><div><br></div><div>--Eric</div><br><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></body></html>