<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Thomas,<div><span class="Apple-tab-span" style="white-space:pre"> </span>We recently changed Chimera so that molecules are initially displayed in a fashion very similar to the "Interactive 1 (ribbons)" preset rather than wireframe. This behavior is controlled by a new "smart initial display" New Molecule preference, which defaults to true. When that preference is true, many of the other preferences in that category are overridden*. So to get back to the behavior you had before, set "smart initial display" to false.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Perhaps this is also the issue with you problem with colordefs, but I don't completely understand your description of that. Are we talking about Command Line startup files? Do you mean that you put a file in the list of Command Line file to read at startup and it's not in the list the next time you start Chimera? (You did click the 'Save' button, right?)</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; "><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>* all other prefs are overridden except for those dealing with initial model color, metal complexes, Mol2 model naming, line width, and ball/stick scale.</div><div><br><div><div>On Aug 24, 2009, at 9:04 AM, Dipl.-Ing. Thomas Mitterfellner wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello!<br>The recent chimera builds seem to ignore my standard molecule settings <br>(ball and stick defaults to stick only) and the files to be read at <br>startup. I normally read in a file with my custom colordefs, but when I <br>set that, close chimera and open it again, this setting is lost.<br>Is this a known issue, or is it just with my installation?</div></blockquote><br></div><br></div></body></html>