<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Andy,<div><br></div><div> The way to use saved positions in an animation is to save a session which includes all the saved positions. Then to make the animation you first open that session and then use the "fly" or "reset" command in a script with those named positions. This is a general method for making animations that works quite well. Setup everything in a session (which models are open, where they are placed, colors, lighting, background color, shadows, …), then just use an animation script to modify a few things. If you instead try to do all the setup in a script with no session it is much harder.</div><div><br></div><div> I don't understand your question about clipping. Normally Chimera does not clip your maps when you zoom in. Only if you turn on clipping or make your view point move right through the map would you see clipping.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><br><div><div>On Jun 11, 2013, at 1:07 AM, Anindito Sen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; font-size: 14pt; position: static; z-index: auto; "><div><span>Hi Tom,</span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span><br></span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span>In the Video tutorial about making a movie of flying through the protein complex - how can I have the positions saved (sav pos) and put it in a script. </span><span style="background-color: transparent; ">The idea is to modify a script that makes a density map rotate (which I already have) and then fly in through that. I can then alter the script accordingly to show different regions of the map (and will not need to type the whole set of
commands). </span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span><br></span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span>Secondly how can modify my script to zoom-in a density map without clipping the region of interest. It is obvious that a major portion of the map will be outside the view but the clipping plane will not move and clip the map (like when we zoom in manually in the Chimera window using the mouse. </span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span><br></span></div><div style="font-size: 19px; "><span>Thanks</span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span><br></span></div><div style="font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal; "><span>Andy</span></div><div></div><div> </div><div><font class="Apple-style-span" color="#0000FF" face="garamond, 'new york', times, serif" size="7"><span class="Apple-style-span" style="font-size: 28px; line-height: 19px; "><b><blockquote type="cite" style="font-family: Helvetica; font-weight: normal; line-height: normal; font-size: 16px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: 16px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: 16px; "><div style="word-wrap:break-word;"><div><font class="Apple-style-span" color="#341dbb" face="'Times New Roman'" size="4"><b>Dr. Anindito Sen (Ph.D)</b></font></div><div><font class="Apple-style-span" color="#341dbb" face="'Times New Roman'" size="4"><b>Department of Cell Biology & Anatomy</b></font></div><div><font class="Apple-style-span" color="#341dbb" face="'Times New Roman'" size="4"><b>Graduate
School of Medicine</b></font></div><div><font class="Apple-style-span" color="#341dbb" face="'Times New Roman'" size="4"><b>University of Tokyo</b></font></div></div></span></span></blockquote></b></span></font></div></div></blockquote></div><br></div></body></html>