<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Alex,<br>
<br>
There are two scripts (placem.py and place.py) on the Chimera
Python scripts web page<br>
<br>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><br>
<br>
that will place models at specified positions. With the placem.py
script you specify the models/maps to open and the x,y,z
translations and optionally the rotation as a quaternion, one model
on each line. You can repeat the same model. The place.py script
places multiple copies of a single model specifying translation and
rotation using a 3 by 4 matrix.<br>
<br>
Tom<br>
<br>
<br>
<br>
<blockquote type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi
Tom, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">When
I told about particles I meant electron-density maps (mrc,
spider, imagic or ccp4 formats). I know all orientation of
the particles and even more all of them a turned already –
what I need is only to place all of them in exact positions.
Of cause I can do it manually, but it is bit boring.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thank
you for the help in advance,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Alex<o:p></o:p></span></p>
<br>
</div>
</blockquote>
<br>
<blockquote
cite="mid:D76DD140FBBE5A49BA76B24EE4A4773C0A68396D@SERV-MAILBOX1.igbmc.u-strasbg.fr"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear colleagues, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I would like to fit
about 300 particles inside of the map according to it
coordinates (X,Y,Z) what I have found before. Is it
possible to make this procedure automatically, such that
program would load one particle, shift it according to its
coordinates (change pixel size if necessary) and so on? <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you in advance, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Alexander<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p><br>
</p>
</div>
</blockquote>
<br>
</body>
</html>