<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Andrew,<div><span class="Apple-tab-span" style="white-space:pre"> </span>At this point the only data that Chimera supports on a per-frame basis is atomic coordinates. So there is only one bfactor per atom, not one bfactor per atom per frame. The only way around this that I can think of is to not to overload the bfactor field but to instead put your per-frame data into a series of <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/defineattrib/defineattrib.html%23attrfile">attribute assignment files</a> that you would read in with the <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/defattr.html">defattr</a> command at every frame. You could then use your rangecolor command after that (with whatever attribute name you used in the assignment file).</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I believe VMD supports per-frame data, if that is of any help.<br></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><br><div><div>On Mar 24, 2009, at 11:15 AM, Andrew M. Simms 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-size: 16px; 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: 0; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I am making some MD movies using the multiple-pdb file format. I am using coloring by attribute, in this case overriding the “bfactor” attribute for my own purposes. The nature of my analysis is such that the bfactor can change from frame to frame. I use this command in the per-frame script:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">rangecolor bfactor,a min white max green<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">However, when I try to make a movie, it appears that the bfactor attribute changes are not reflected in the animation. If I look at generated structures individually they are fine.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Is there something special I need to specify in per-frame script?<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks!<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">--Andrew<o:p></o:p></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></span></blockquote></div><br></div></body></html>