<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Heather -<br>
<br>
From your Coot window, you can go to Edit->Preferences, then
select the "Map Colours" tab in the resulting window. You should
see radio buttons for "Coot colours" and "O colours". The way
these work is that you select the desired colo(u)r for the
positive difference density (e.g. green). The negative contour is
then 120 degrees ahead (clockwise) on the color wheel if you
choose Coot colors, or 120 degrees behind if you choose O colors.<br>
<br>
It looks to me like you want positive to be green, and negative to
be red. So I think you want Coot colors, and positive set to
green. At the moment, it appears that you have O colors.<br>
<br>
I have no idea if your selections will be kept the next time
Phenix opens a window for you. Probably not.<br>
<br>
Hope that helps,<br>
<br>
Matt<br>
<br>
<br>
On 8/28/13 11:22 AM, Heather L Condurso wrote:<br>
</div>
<blockquote
cite="mid:CAPWtQMxDtR4sFTrNCaCM-zCjD=sbTDW4vCfiN+Ew4-xLA1wV5w@mail.gmail.com"
type="cite">
<div dir="ltr">I can go into map colors and change them to
whatever color I want, but if I try and make what I imagine
should be + green, then - are royal blue. The only way I can
get red and green is if the - are green, then the positives are
red. I will just pretend royal blue is red for now. If you
come up with anything let me know.</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Aug 28, 2013 at 10:57 AM,
Nathaniel Echols <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:nechols@lbl.gov"
target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="im">On Wed, Aug 28, 2013 at 7:51 AM, Heather
L Condurso <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:condurso@bc.edu" target="_blank">condurso@bc.edu</a>></span>
wrote:<br>
</div>
<div class="gmail_quote">
<div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">I'm having an issue that when I
launch coot from the phenix refine gui it loads
the pdb and mtz fine, but the FoFc map colors
are green and royal blue. When I open coot
first and then load the pdb and mtz files, the
FoFc map colors are green and red, but the blobs
that were green in the phenix loaded maps are
now red and what was royal blue is now green.
Has anyone else had this issue? I am running a
mac with OS X 10.6.8 and coot 0.6.1 and phenix
1.8.2-1309. I have an identical mac running all
the same versions and everything loads green and
red as expected. Is there a parameter file
somewhere that tells coot how to display the
phenix maps that may provide a clue as to what
is going on?</div>
</blockquote>
<div><br>
</div>
</div>
<div>See Preferences->Colors. If that doesn't seem
consistent with what you see in Coot, we may have a
bug...</div>
<div><br>
</div>
<div>-Nat</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374</pre>
</body>
</html>