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Dear Eric,<br>
<br>
By the way, thank you very much for having added the possibility to
invert the configuration of chiral atoms in Chimera in response to
our suggestion (#9474: RFE: chirality inversion). That will also be
very useful!<br>
<br>
Have a nice day,<br>
Vincent<br>
<br>
<br>
On 11/16/2011 08:31 PM, Eric Pettersen wrote:
<blockquote
cite="mid:4639461D-7E87-494A-AF4D-1DB6386AB883@cgl.ucsf.edu"
type="cite">Hi David,
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>I'd
be happy to help you get your extension working. Do you
envision your extension being a separate tool that provides its
own interface, or instead being integrated into the Rotamers
tool and simply being listed as another possible rotamer
library? I'm guessing the latter since I don't think you'd care
about the format of Chimera's rotamer libraries otherwise, but
let me know so I know what kind of guidance to provide. If
integrating with Rotamers, I will need to change some code
[which I'm perfectly happy to do!] since Rotamers only handles
standard amino acids right now.</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>You
should probably omit chimera-dev on any replies since we'll be
getting into hairy minutiae that is unlikely to be of interest
to others.</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>Speaking
of hairy minutiae, the rotamer files aren't encrypted per se,
but have been converted to a binary format that can be read a
lot faster by Chimera. I have attached the Python scripts that
were use to convert backbone-dependent files and
backbone-independent files into the zip archives that Chimera
uses. They should "just work" on your files since you use the
Dunbrack format.</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>Anyway,
let me know how you want your extension to work and I can
provide the proper know-how for you to get going.</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
</div>
<div>
<div style="margin: 0px; font-size: 16px;"><font style="font:
16px Helvetica;" face="Helvetica" size="5">
Eric Pettersen</font></div>
<div style="margin: 0px; font-size: 16px;"><font style="font:
16px Helvetica;" face="Helvetica" size="5">
UCSF Computer Graphics Lab</font></div>
<div style="margin: 0px; font-size: 16px;"><font style="font:
16px Helvetica;" face="Helvetica" size="5">
<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div>
<div><font style="font: 16px Helvetica;" face="Helvetica"
size="5"><br>
</font></div>
<div>
<div>On Nov 16, 2011, at 12:52 AM, david gfeller wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Dear Chimera developer,<br>
<br>
I've been working recently on a database on non-natural
sidechains (<a moz-do-not-send="true"
href="http://www.swisssidechain.ch">http://www.swisssidechain.ch</a>).
Among else, we've developed a novel approach to accurately
predict rotamers and our paper will be submitted within a
few days.<br>
<br>
I'd be very interested to develop a Chimera extension to
visualize them (so far, we only have a PyMOL plug-in). I
have rotamer library files in the same format as the
Dunbrack 2002 rotamer library for each of the >200
sidechains included in my database. However, it appears that
rotamer files (dependentRotamerData.zip) are encrypted in
Chimera and I could not figure out how this encryption is
done.<br>
<br>
I was wondering if you could advise me something to help me
(especially whether there are some hard-coded part that
would need to be modified to include new sidechains in
Chimera) and if you'd be interested in such an extension.</blockquote>
<br>
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