<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0" style="position: relative; z-index: 0; "><tbody><tr><td valign="top" style="font: inherit;">Thanks Eric, but just to follow up on the surf sel command,<br><br>It displays the surface for the selected residues, <br><br>does it assign solvent-excluded and solvent-accessible surface areas per atom and residue to attributes named <b>areaSES</b> and <b>areaSAS</b> to the selected residues or to the whole protein?.<br><br>after I do "surf sel" I have select:/areaSAS > 50 , looks like it selects for the whole protein. Shouldn't it show only for the selected surface region.<br><br></td></tr></tbody></table></blockquote><br><table cellspacing="0" cellpadding="0" border="0" style="position: relative; z-index: 0; "><tbody><tr><td valign="top" style="font: inherit;">Hi Thiru,<br><span class="Apple-tab-span" style="white-space:pre"> </span>Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>sel :/areaSAS > 50 & @/surfaceDisplay<br><br>--Eric<br><span class="Apple-tab-span" style="white-space:pre"> </span></td></tr></tbody></table><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0" style="position: static; z-index: auto; "><tbody><tr><td valign="top" style="font: inherit;">Thanks<br><br>-Thiru<br><br>--- On <b>Wed, 10/7/09, Eric Pettersen <i><<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>Subject: Re: Displaying Surface For Selected Residues<br>To: "Thiruvarangan Ramaraj" <<a href="mailto:thiruvaranganr@yahoo.com">thiruvaranganr@yahoo.com</a>><br>Date: Wednesday, October 7, 2009, 5:14 PM<br><br><div id="yiv1205319991">Yes, most commands work on everything if you don't specify what to work on. For instance "color red" colors everything red whereas "color red sel" colors the selection red.<div><br></div><div>--Eric</div><div><br><div><div>On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;" valign="top">Worked fine, Thanks, Eric<br><br>-Thiru<br><br>--- On <b>Wed, 10/7/09, Eric Pettersen <i><<a rel="nofollow" ymailto="mailto:pett@cgl.ucsf.edu" target="_blank" href="/mc/compose?to=pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Eric Pettersen <<a rel="nofollow" ymailto="mailto:pett@cgl.ucsf.edu" target="_blank" href="/mc/compose?to=pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>Subject: Re: Displaying Surface For Selected Residues<br>To: "Thiruvarangan Ramaraj" <<a rel="nofollow" ymailto="mailto:thiruvaranganr@yahoo.com" target="_blank" href="/mc/compose?to=thiruvaranganr@yahoo.com">thiruvaranganr@yahoo.com</a>><br>Date: Wednesday, October 7, 2009, 5:04 PM<br><br><div id="yiv151915881">"surface sel"<div><br></div><div>--Eric</div><div><br><div><div>On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">Hi Eric,<br><br>I have a protein with a few residues selected, and I wanted to show surface only on the selected residues, when I go to Actions - Surface -Show , it shows surface only for the selected residues, but when I use the command surface on the command line it shows the surface for the entire protein. Is there a command line option to show surface only for the selected residues on the protein.<br><br>Thanks<br><br>Thiru<br><br>--- On <b>Thu, 10/1/09, Eric Pettersen <i><<a rel="nofollow">pett@cgl.ucsf.edu</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Eric Pettersen <<a rel="nofollow">pett@cgl.ucsf.edu</a>><br>Subject: Re: [Chimera-users] Solvent Accessible Surface Area<br>To: "Thiruvarangan Ramaraj" <<a rel="nofollow">thiruvaranganr@yahoo.com</a>><br>Cc: "UCSF Chimera Mailing List" <<a rel="nofollow">chimera-users@cgl.ucsf.edu</a>><br>Date: Thursday, October 1, 2009, 3:38 PM<br><br><div class="plainMail">Oops, spotted a bug in the script. This line:<br><br>out = open(os.path.expanduser("~/out", "w"))<br><br>should be:<br><br>out = open(os.path.expanduser("~/out"), "w")<br><br>--Eric<br><br><br></div></blockquote></td></tr></tbody></table><br> </blockquote></div><br></div></div></blockquote></td></tr></tbody></table><br> </blockquote></div><br></div></div></blockquote></td></tr></tbody></table><br> </blockquote></div><br></body></html>