<!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 text="#000000" bgcolor="#ffffff">
Chimera does not have an analogous algorithm. If you could send me
a reference, it might not be hard to write a small script. For
instance, adding hydrogen bonds for strands will help stability and
the Chimera commands to do that would be:<br>
<br>
select strand<br>
findhbond selRestrict strand<br>
<br>
or with the menus:<br>
<br>
Select / secondardary structure / strand<br>
Tools / Structure Analysis / FindHBond<br>
Only find H-bonds with both ends selected<br>
OK<br>
<br>
HTH,<br>
<br>
Greg<br>
<br>
On 04/08/2011 11:03 AM, Bilal Asif wrote:
<blockquote
cite="mid:BANLkTim6ZrG2B-4DWvOVAhYr5Ebmfcapaw@mail.gmail.com"
type="cite">Thanks.
<div><br>
</div>
<div>In regards to adding fake bonds...I know Jmol has an
algorithm for struts that allows stability in manipulated
proteins. Does Chimera have an analogous algorithm to provide
support for unstable structures? <br>
<br>
<div class="gmail_quote">On Fri, Apr 8, 2011 at 1:44 PM, Greg
Couch <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> For a ZCorp printer
that has the ZPrint software, I'd recommend exporting VRML
files from Chimera. The advantage of VRML over STL is
that VRML includes the color information and that Chimera
is not as good as ZPrint at decimating spheres and
cylinders into appropriate sized triangles for 3D
printing. Use the File / Export Scene dialog to export
VRML files from chimera or use the export command. And be
aware that the cylinders used for bonds might need to be
thickened so they don't break. And you might need to add
fake bonds to make the structure physically stable.<br>
<br>
HTH,<br>
<br>
Greg
<div>
<div class="h5"><br>
<br>
On 04/08/2011 10:16 AM, Bilal Asif wrote: </div>
</div>
<blockquote type="cite">
<div>
<div class="h5">Hi Elaine,
<div><br>
</div>
<div>Thank you for such a comprehensive email! </div>
<div><br>
</div>
<div>We had some follow up questions, however, which
we were hoping you would be able to answer. We are
attempting to use Chimera to model proteins, and
then print them using a 3D printer (ZCorp
software). The following file types are compatible
with the printer software:</div>
<div><br>
</div>
<div>STL</div>
<div>VRML</div>
<div>3DS</div>
<div>ZPR</div>
<div>PLY</div>
<div><br>
</div>
<div>Can Chimera save in any of these formats, that
can be used to print proteins? How would one save
the session as one of these? Additionally, I had a
question about saving the session in Chimera, to
preserve labels and colored atoms. Is such a saved
session a Chimera-specific file, where it cannot
be read by external programs?</div>
<div><br>
</div>
<div>Thank you for your time. </div>
<div><br>
</div>
<div>Bilal Asif</div>
<div>Stony Brook University, NY</div>
</div>
</div>
<pre><fieldset></fieldset>
_______________________________________________
Chimera-users mailing list
<a moz-do-not-send="true" href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a>
<a moz-do-not-send="true" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<font color="#999999">Bilal Asif</font><br>
</div>
</blockquote>
<br>
</body>
</html>