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Hi Ibrahim,<div><span class="Apple-tab-span" style="white-space:pre"> </span>As Bala pointed out, IED in VMD may well be the way to go for now. Also, the "porcupine needles" can be accomplished with BILD, as Elaine mentioned. I've attached a script that reads a file of displacements and applies them to the CAs of a structure. Obviously, there should be as many lines in the file as there are CAs in the structure. Each line should consist of 3 numbers, the X, Y, and Z displacements. Since the script only modifies the CAs, you should probably only be displaying the CAs -- the rest of the structure will be out of position. You may need to edit the script to put in the name of the file with the displacements, otherwise it will use a file named "displacements" in the same directory as the script. You run the script by simply opening it with File...Open or the "open" command.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>We are working on closer coordination between Amber and Chimera, with the help of Wei Zhang. He has already contributed one tool, Solvate, which uses sleap to solvate a system. Solvate is available in daily builds. In the short term he hopes to write tools to add ions and write parmtop files. Longer term goals are to include the minimization and MD functionality of NAB, and ptraj trajectory analysis.</div><div><br></div><div>--Eric</div><div><span class="Apple-tab-span" style="white-space:pre"> </span><br><div> <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; "><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"></span> </div><div></div></div></body></html>