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<font size="+1"><font face="monospace">Hi Tom, <br>
<br>
I figured it out. <br>
My chain and volume were correctly defined, it is the original
coloring of the model when first opened in ChimeraX that was
different. <br>
For some reason, "open 7lup" opens the pdb in ball and stick
with one color per chain. <br>
When I open my PDB, it opens it in sticks with one color per
atom type. <br>
<br>
Using the color zone command colors according to the color of
the PDB, thus by atom type. Cf the 2 attached pictures for
clarity. <br>
<br>
If I say:<br>
color #1/A yellow<br>
color zone #2 near #1 <br>
<br>
then I can change the colors as I want and color chain A in
yellow. <br>
<br>
I'm using </font></font><font size="+1"><font face="monospace"><span
style="color: rgb(0, 0, 0); font-family: "Times New
Roman"; font-size: medium; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: 400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;">version 1.2 (2021-04-27)<br>
<br>
Best<br>
Vincent<br>
<br>
</span></font></font>
<div class="moz-cite-prefix">Le 20/09/2021 à 19:58, Tom Goddard a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:720A1C8F-1650-4DB4-A4A2-8DADBC4906D8@sonic.net">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Vincent,
<div class=""><br class="">
</div>
<div class=""> Check that your map is model #2 and your atomic
structure is model #1 by looking at the id numbers in the Models
panel. Also if you hover the mouse over an atom you can check
that your atomic structure as chain A.</div>
<div class=""><br class="">
</div>
<div class=""> I see that If you get the model numbers wrong the
command does not warn you that nothing was colored. I will fix
that so it gives a warning.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 20, 2021, at 2:45 AM, vincent Chaptal
via ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu" class=""
moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta charset="UTF-8" class="">
<font style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration: none;"
class="" size="+1"><font class="" face="monospace">Dear
ChimeraX users,<span class="Apple-converted-space"> </span><br
class="">
<br class="">
I just subscribed so apologies if this has been asked
before.<span class="Apple-converted-space"> </span><br
class="">
<br class="">
When is type the command: color zone #2 near #1/A
distance 5 sharpEdges false farColor blue<br class="">
<br class="">
I have the volume #2 in blue with chain A colored by
atom type: i.e. with carbons in sand, oxygens in red,
nitrogens in blue.<span class="Apple-converted-space"> </span><br
class="">
<br class="">
I tried to follow the tutorial on youtube, downloading
the model and emdb like in the tutorial, and it does
work like the tutorial, meaning colored by chain.<span
class="Apple-converted-space"> </span><br class="">
<br class="">
I am wodering what is going on and how to fix it? I've
seen this behavior for my protein, on a PDB refined
from Phenix, or from a download from the rcsb.<span
class="Apple-converted-space"> </span><br class="">
I don't see anything special on the PDB, all the atoms
are listed normally.<span
class="Apple-converted-space"> </span><br class="">
<br class="">
<br class="">
Is it possible to assign a specific color per chain
using this command?<span class="Apple-converted-space"> </span><br
class="">
<br class="">
<br class="">
Thank you for your help.<span
class="Apple-converted-space"> </span><br class="">
best<br class="">
Vincent<br class="">
<br class="">
<br class="">
<br class="">
</font></font><span style="caret-color: rgb(0, 0, 0);
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<div class="moz-signature" style="caret-color: rgb(0, 0,
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-webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span
class="s1" style="-webkit-font-kerning: none;">Vincent
Chaptal, PhD</span></div>
<div style="margin: 0px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
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normal; font-family: Helvetica;
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-webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span
class="s1" style="-webkit-font-kerning: none;">Director
of GdR APPICOM</span></div>
<div style="margin: 0px; font-style: normal;
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font-stretch: normal; font-size: 12px; line-height:
normal; font-family: Helvetica;
-webkit-text-stroke-width: initial;
-webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span
class="s1" style="-webkit-font-kerning: none;">Drug
Resistance and Membrane Proteins Lab</span></div>
<div style="margin: 0px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
font-stretch: normal; font-size: 12px; line-height:
normal; font-family: Helvetica;
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14px;" class=""><span class="s1"
style="-webkit-font-kerning: none;"></span><br
class="">
</div>
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-webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span
class="s1" style="-webkit-font-kerning: none;">MMSB
-UMR5086</span></div>
<div style="margin: 0px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
font-stretch: normal; font-size: 12px; line-height:
normal; font-family: Helvetica;
-webkit-text-stroke-width: initial;
-webkit-text-stroke-color: rgb(0, 0, 0);" class=""><span
class="s1" style="-webkit-font-kerning: none;">7
passage du Vercors<span
class="Apple-converted-space"> </span></span></div>
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<p class="p1"><span class="s1">Vincent Chaptal, PhD</span></p>
<p class="p1"><span class="s1">Director of GdR APPICOM</span></p>
<p class="p1"><span class="s1">Drug Resistance and Membrane
Proteins Lab</span></p>
<p class="p2"><span class="s1"></span><br>
</p>
<p class="p1"><span class="s1">MMSB -UMR5086</span></p>
<p class="p1"><span class="s1">7 passage du Vercors<span
class="Apple-converted-space"> </span></span></p>
<p class="p1"><span class="s1">69007 LYON</span></p>
<p class="p1"><span class="s1">FRANCE</span></p>
<p class="p1"><span class="s1">+33 4 37 65 29 01</span></p>
<p class="p1"><span class="s1"><a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a></span></p>
<p class="p1"><span class="s1"><a class="moz-txt-link-freetext" href="http://mmsb.cnrs.fr/en/">http://mmsb.cnrs.fr/en/</a></span></p>
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