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Re: [PyMOL] Color backbone amide nitrogen
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From: Marko H. <mh...@ca...> - 2018-07-23 17:50:24
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<tt>The problem is that yo</tt><tt>u are </tt><tt>not </tt><tt>visualising
the backbone nitr</tt><tt>ogen</tt><tt>s</tt><tt>.</tt><tt> Y</tt><tt>ou
on</tt><tt>ly show the side </tt><tt>chains as sticks and the
back</tt><tt>bone is </tt><tt>shown as cartoons.These schematic
representations of secondary structure are drawn us</tt><tt>ing</tt><tt>
</tt><tt>Calp</tt><tt>ha </tt><tt>atom</tt><tt> positions and (t</tt><tt>ypically)
inherit the co</tt><tt>lour of the </tt><tt>Calphas. </tt><tt> </tt><tt>If
you show the backbone as sticks, the nitrogens will be visible and
they will have colour. </tt><tt>Same goes for backbone oxygens
which are similarly hidden in your image, but are coloured in the
side chain at the bottom of the image. <br>
</tt><tt><br>
</tt><tt>hth, Marko</tt><br>
<br>
<div class="moz-cite-prefix">On 23/07/2018 18:17, Santrupti Nerli
wrote:<br>
</div>
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cite="mid:202...@uc...">
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Hi,
<div class=""><br class="">
</div>
<div class="">I want to color backbone nitrogen atoms together
with side-chain nitrogen atoms. The side-chain nitrogens get the
color, however the backbone nitrogens don’t (see below; I have
selected backbone nitrogens). I tried some options such as</div>
<div class=""><br class="">
</div>
<div class="">select bb, name n</div>
<div class="">color by element </div>
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes"
id="D27751EC-DA9B-450C-AB41-1005FF676831"
src="cid:par...@ca..." class=""></div>
<div class=""><br class="">
</div>
<div class="">But, the backbone nitrogens aren’t getting colored.
Is there a way to color them without showing them as spheres?</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot.</div>
<br>
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<pre class="moz-signature" cols="72">--
Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
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