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Thanks Elaine and Tom for helpful replies!<div><br><div><div>On Oct 2, 2009, at 5:31 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Cathy,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Regarding #3, eventually we would like to allow users to define their own presets.<span class="Apple-converted-space"> </span>For now, I suggest making an alias such as with the command:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">alias stuff preset apply int 1; set bg_color white</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and then later the command "stuff" (or whatever you named it) will do what you want.<span class="Apple-converted-space"> </span>For the alias to be in effect automatically whenever you use Chimera, put it in a file along with any other aliases, color definitions, etc. you might want, and use the Preferences, Command Line category to specify that file to be read at startup.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Regarding #4, alternatives for clearing the selection are</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- keyboard shortcut cs</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- command ~sel</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- picking nothing, i.e. Ctrl-click in empty area of graphics window</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I hope this helps,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine C. Meng, Ph.D.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Pharmaceutical Chemistry</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, San Francisco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear Chimera Team,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I have been using Chimera fairly intensively in recent days with good success. <span class="Apple-converted-space"> </span>Just wanted to pass along a short list of features I wish were available.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(maybe some are already available in Chimera or there are workarounds but I<span class="Apple-converted-space"> </span>haven't been able to figure them out...).<span class="Apple-converted-space"> </span>I'm using the current production release (1.3) mac osx (X11).</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(1) A way "close" the command line at the bottom of the view window<span class="Apple-converted-space"> </span>(among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open).</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(2) An "undo" button for "fit in map"<span class="Apple-converted-space"> </span>(restore model to position before fit)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(3) Fine tuning of the "preset" views<span class="Apple-converted-space"> </span>-- interactive (ribbons) is something I use frequently but I'd prefer a white background.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cathy</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; 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; -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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); 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; -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; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div><span class="Apple-style-span" style="font-family: Georgia; font-size: 13px; ">--o----o-o-o-|--o-o-o-|--- </span></div><div><a href="http://rutchem.rutgers.edu/~lawson">http://rutchem.rutgers.edu/~lawson</a></div><div>new phone #: 732 445 5494</div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span><br class="Apple-interchange-newline"></span></span> </div><br></div></body></html>