<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Sorry, these duplicate messages from Chris were accidentally approved by the list moderator (messages from non-subscribed addresses go into holding for approval). Please ignore!<div><br></div><div>--Eric</div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 16px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div><div><div>On Jan 28, 2012, at 11:07 PM, Chris Tomlinson wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello,<div><br></div><div>Thank you very much for the information. The combination of Chimera and Blender works quite well. I find that it is all too easy to create models that are much too complex for the iPad however.</div><div><br></div><div>Chris</div><div><br></div><div><br><div><div>On Jan 29, 2012, at 9:28 AM, Evan Kantrowitz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>This is the way I got it to work, I exported Chimera scene to VRML (.wrl). </div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Next you need blender. You can download it from</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(69, 83, 252); "><span style="text-decoration: underline"><a href="http://www.blender.org/download/get-blender/"><font class="Apple-style-span" size="3">http://www.blender.org/download/get-blender/</font></a></span></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Then Open Blender. In the upper right corner in the Scene section</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">right click on Lamp and delete it</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">right click on Cube and delete it</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">right click on Camera and delete it</font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Save this file so you don't have to do this every time. I called mine empty_blender_file.blend</font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Either open empty_blender_file.blend or continue from above and read in the the .wrl file from Chimera</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">File -> import->X3D Extensible 3D (.x3d/.wrl)</font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">this reads in the file</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">In Blender you need to delete the three lights that came in from Chimera called TOPO, TOPO.001 and TOPO.002</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><span class="Apple-style-span" style="font-size: medium; ">In the upper right corner in the Scene section</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">right click on TOPO and delete it</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">right click on TOPO.001 and delete it</font></div>right click on TOPO.002 and delete it</font></div><div><font class="Apple-style-span" size="3"><font class="Apple-style-span" color="#333233"><br></font></font>Now you need to move around the viewport to get it centered</div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); ">In the upper right corner in the Scene section</span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); ">click on the Viewport</span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); ">then press number pad 0</span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); ">Press the cube icon below the Scene section</span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); "><br></span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); ">Now in the transform section move the location x,y,z. When you have it the way you want it is ready for export.</span></div><div><span class="Apple-style-span" style="color: rgb(51, 50, 51); "><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">File->export->collada (.dae)</font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Done. This file will read into iBooks Author and have somewhat uniform lighting. By the way, .dae files can be opened an checked in Preview. Its easier than going back and forth into the iPad, since you can rotate the image in Preview.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Here is a link to a .dae file of 1crn that you can import into iBooks Author or Preview</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><a href="http://dl.dropbox.com/u/4300550/1crn2_mod.dae">http://dl.dropbox.com/u/4300550/1crn2_mod.dae</a></font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Hope this helps, let me know if it works for you and if you have any suggestions.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Finally, someone needs to write a one step VRML and/or X3D to collada converter that will work with PyMol and Chimera etc.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">PS It was a little easier from PyMol, if your interested see the post at <a href="https://discussions.apple.com/thread/3670156?start=0&tstart=0">https://discussions.apple.com/thread/3670156?start=0&tstart=0</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">PSS. Okino Computer Graphics makes a .wrl and .x3d to .dae converter <a href="http://www.okino.com/">http://www.okino.com</a></font></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 13.0px 'Lucida Grande'; color: #333233"><font class="Apple-style-span" size="3"> </font></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal 'Lucida Grande'; color: rgb(51, 50, 51); "><font class="Apple-style-span" size="3">Have fun!</font></div></div></div></blockquote></div></div></div></blockquote></div></div><br><br></body></html>