<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta content="text/html; charset=utf-8">
</head>
<body class="" style="word-wrap:break-word; line-break:after-white-space">
<div dir="auto">Hi thanks for your answer.
<div dir="auto"><br>
</div>
<div dir="auto">But i actually want to apply the command to all frames in order to see the neighbors through the simulation, to build also a movie. How should i do that?</div>
<div dir="auto"><br>
</div>
<div dir="auto">In any case i solved it by using an external alias in the command line</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thanks?</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Jan 30, 2020 21:13, Eric Pettersen <pett@cgl.ucsf.edu> wrote:<br type="attribution">
</div>
</div>
<div>Hi Fabian,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>By typing ‘1’ into the entry field of ’Substitute text [1] with frame number’, any ‘1’ in your script will be replaced by the frame number, so by frame 96 the text ’sel :1000 zr<5’ becomes
’sel :96000 zr<5’. I’m guessing you want your command executed only on frame 1. To do that, as it says just above the ’Script’ area, prepend the command with ‘#:’, e.g.:</div>
<div class=""><br class="">
</div>
<div class="">#1:~disp</div>
<div class="">#1:rib</div>
<div class=""><i class="">etc.</i></div>
<div class=""><br class="">
</div>
<div class="">Also, you will need to change that entry field back to something that isn’t found in your script,
<i class="">e.g.</i> “<FRAME>”.</div>
<div class=""><br class="">
</div>
<div class="">—Eric </div>
<div class=""><br class="">
<div class="">
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; text-decoration:none">
<span class="Apple-tab-span" style="white-space:pre"><br class="Apple-interchange-newline">
</span>Eric Pettersen</div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; text-decoration:none">
<span class="Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; text-decoration:none">
<br class="">
</div>
<br class="Apple-interchange-newline">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 29, 2020, at 4:21 AM, Fabian Glaser <<a href="mailto:fglaser@technion.ac.il" class="">fglaser@technion.ac.il</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="word-wrap:break-word; line-break:after-white-space">
<div class="" style="word-wrap:break-word; line-break:after-white-space">Dear Chimera developers,
<div class=""><br class="">
</div>
<div class="">I think I have found abug in the MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue
number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case
96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Fabian</div>
<div class=""><br class="">
</div>
<div class=""><span id="cid:574D5092-B544-4D5A-BAAF-4E9CB1E0B5E9@bi.technion.ac.il"><Screenshot 2020-01-29 14.17.26.png></span><br class="">
<div class="">
<div dir="auto" class="" style="letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; word-wrap:break-word; line-break:after-white-space">
<div dir="auto" class="" style="letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; word-wrap:break-word; line-break:after-white-space">
<div dir="auto" class="" style="letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; word-wrap:break-word; line-break:after-white-space">
<div dir="auto" class="" style="letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; word-wrap:break-word; line-break:after-white-space">
<div dir="auto" class="" style="word-wrap:break-word; line-break:after-white-space">
<div class="" style="font-variant-caps:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<br class="">
Best,<br class="">
<br class="">
Fabian<br class="">
<br class="">
Fabian Glaser PhD<br class="">
<br class="">
Bioinformatics Knowledge Unit - BKU<br class="">
The Lorry I. Lokey Center for Life Sciences and Engineering<br class="">
Technion - Israel Institute of Technology, Haifa, Israel<br class="">
Web <a href="https://lokey.technion.ac.il/bioinformatic-knowledge-unit/" class="">https://lokey.technion.ac.il/bioinformatic-knowledge-unit/</a><br class="">
Tel +972 (0) 4 8293701<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
</div>
</div>
_______________________________________________<br class="">
Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">
Chimera-users@cgl.ucsf.edu</a><br class="">
Manage subscription: <a href="https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cfglaser%40technion.ac.il%7Cbd7960bb8fd54fef0e4608d7a5b88516%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637160084252741437&sdata=UYxzyRshkjlTfwVXEqUl7a46eQESa5%2FNGjcBvGMhLVQ%3D&reserved=0" originalsrc="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" shash="dUdUS4Yt6q8rUKRj0ti9PnViCWdiVjeCJXCWtm4Cc5TF1NTMKKS40fAzW74CYOgcdDshw3qN8or9HxLFXaPEVlo3RLQB/fFOxFj4cyeI+J8o+5TMxKs+q4XFrgkJs1CRudKlX78+nJ2iYeSsjezDLhwozihxcpI006bSZn/BwoE=" class="">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</body>
</html>