<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Exchange Server">
<!-- converted from text --><style><!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #800000 2px solid; } --></style>
</head>
<body>
<style>
<!--
@font-face
{font-family:"Cambria Math"}
@font-face
{font-family:Calibri}
p.x_MsoNormal, li.x_MsoNormal, div.x_MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif}
a:link, span.x_MsoHyperlink
{color:blue;
text-decoration:underline}
a:visited, span.x_MsoHyperlinkFollowed
{color:#954F72;
text-decoration:underline}
.x_MsoChpDefault
{}
@page WordSection1
{margin:1.0in 1.0in 1.0in 1.0in}
div.x_WordSection1
{}
-->
</style>
<div lang="EN-US" link="blue" vlink="#954F72">
<div class="x_WordSection1">
<p class="x_MsoNormal">Hi Elaine,</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Best,</p>
<p class="x_MsoNormal">Ryan Harlich</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows 10</p>
<p class="x_MsoNormal"> </p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, July 11, 2019 12:49:19 PM<br>
<b>To:</b> Ryan Harlich<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Finding dimensions of density map</font>
<div> </div>
</div>
</div>
<font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi Ryan,<br>
The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates</a>><br>
<br>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only
as a PDB file. E.g. if the volume model is #4, command:<br>
<br>
meshmol #4 1<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html</a>><br>
<br>
then,<br>
… Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box<br>
...use “write” command or File… Save PDB with their respective option to save only the selected part<br>
<br>
I hope this helps,<br>
Chimera ;-)<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:<br>
> <br>
> Hi Chimera,<br>
> <br>
> I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about
doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?<br>
> <br>
> Best,<br>
> Ryan Harlich<br>
<br>
</div>
</span></font>
</body>
</html>