[Jmol-developers] [ jmol-Bugs-3517548 ] unaccurate plot of an Isosurface MAPPED with a variable

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Bugs item #3517548, was opened at 2012-04-13 11:42
Message generated for change (Comment added) made by hansonr
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Category: Application
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Romuald Poteau (romualdpoteau)
Assigned to: Bob Hanson (hansonr)
Summary: unaccurate plot of an Isosurface MAPPED with a variable

Initial Comment:
I am not sure if it is a bug or my inability to use the isosurface MAP feature.
Please find the description in the text
Sincerely yours,
Romuald Poteau

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>Comment By: Bob Hanson (hansonr)
Date: 2012-04-14 07:38

Message:
I'll need a .JMOL file created from that view you show in the PDF. Just
use

write toBob.jmol

and send me that, please.  ha...@st...

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Comment By: Romuald Poteau (romualdpoteau)
Date: 2012-04-13 23:40

Message:
"It's possible that your data does not have many points within
that last color group".

It is the case, which makes to the interest to visualize the specific
behavior of these two atoms.
Surprisingly, if I set the range within the values of these atoms, I don't
get the expected colors at all.

By the way, if I do so, I will not follow the scale given in the pdf file
and what I need is a strict correspondence color <-> property, in the range
of interest. If necessary, I can send you my data and a tentative of
expected colors roughly drawn with Gimp.

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Comment By: Bob Hanson (hansonr)
Date: 2012-04-13 13:26

Message:
Tests on =1CRN mapping a variable assigned to temperature using 

set userColorScheme [x000073] [x0003B6] [x0212FF] [x7E7AF8] [xD2D6F8]
[xFFFFFF] [xFFD0D0] [xF87D6A] [xF30004] [x990003] [x730213]
x = {*}.temperature.all
isosurface s1 sasurface map variable x
color $s1 "user" range 0 20

works fine. It's possible that your data does not have many points within
that last color group. If you want to emphasize that group, then set your
range somewhat within that range to force more colors to "saturate" the
spectrum.

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