<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 28, 2011, at 11:44 AM, Beale, John wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div bgcolor="white" background="cid:image001.jpg@01CBD74D.96497040" lang="EN-US" link="blue" vlink="purple" style="margin-left: 37.5pt; "><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 37.5pt; font-size: 12pt; font-family: 'sans serif', serif; color: black; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); ">Hello,<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 37.5pt; font-size: 12pt; font-family: 'sans serif', serif; color: black; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 37.5pt; font-size: 12pt; font-family: 'sans serif', serif; color: black; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); ">Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation.<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 37.5pt; font-size: 12pt; font-family: 'sans serif', serif; color: black; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><o:p> </o:p></span></div></div></div></span></blockquote><br></div><div>Hi John,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I pretty sure this requires some (possibly simple) Python scripting. No script can really be written though without the answer to this question: what is your definition of "internal"?</div><div><br></div><div>--Eric</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><br></body></html>