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<p>Dear Tom,</p>
<p> thank you very much for these explanations. I shall try in
the next days and report!</p>
<p>bw Dieter<br>
</p>
<pre class="moz-signature" cols="72">------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at">dieter.blaas@meduniwien.ac.at</a>
------------------------------------------------------------------------</pre>
<div class="moz-cite-prefix">Am 18.06.2018 um 19:48 schrieb Tom
Goddard:<br>
</div>
<blockquote type="cite"
cite="mid:AF8EE21F-3DB4-4A43-BA6A-0AF760D1B1FB@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Dieter,
<div class=""><br class="">
</div>
<div class=""> This cannot be done easily. To do it you would
want a a gradient norm map, then you could mask your map setting
all the values to zero where the gradient norm is small. The
surface color tool you are using does not compute a gradient
norm map — it just computes gradient norm values on the surface
which is not good enough for your use. Even if you get the
gradient norm map, I see lots of red in the blue region so
masking is going zero many grid points in the interior of the
virus. You could try to smooth (Gaussian filter) the gradient
norm map to avoid that. Finally it is possible to get the
gradient norm (squared) by just using "vop subtract”, “vop
multiply” and “vop add”. There are a lot of steps to it —
basically you do a center difference along each axis, in other
words take 2 copies of the map shift one by 1 voxel along -x and
the other by 1 voxel in the +x direction, then subtract them.
Do the same along y and z axes. The 3 resulting maps give you
the 3 components of the gradient vector. Square each component
(vop multiply map times itself), then sum the 3 squared
components and you have the norm squared. There is no
square-root operator so hopefully the norm squared would
suffice.</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 Jun 15, 2018, at 10:23 PM, Blaas Dieter
<<a href="mailto:dieter.blaas@meduniwien.ac.at"
class="" moz-do-not-send="true">dieter.blaas@meduniwien.ac.at</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Dear Elaine,</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class=""> thanks a lot! Here it is! I open
a volume, colour it according to 'gradient norm' and
would like to save the red or the blue part of the whole
(not just the half of the virus shown!</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">bw Dieter</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">On 2018-06-16 00:06, Elaine Meng
wrote:</span><br style="caret-color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 12px; 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="">
<blockquote type="cite" style="font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"
class="">Dear Dieter,<br class="">
An isosurface is just the surface of a density map
showing a certain<br class="">
level, i.e. the “surface” display in Volume Viewer.<br
class="">
Do you have one map or two maps? I tried to ask that by
saying “if I<br class="">
understand correctly” in my previous message. I thought
you were just<br class="">
coloring the isosurface of one density map by the values
in a second<br class="">
map, where the second map is gradient norm map.<br
class="">
It might help if you attached a picture of the display
and Volume<br class="">
Viewer dialog. “blue part” and “red part” are
ambiguous.<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D.<br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<blockquote type="cite" class="">On Jun 15, 2018, at
2:51 PM, Dieter Blaas <<a
href="mailto:dieter.blaas@meduniwien.ac.at" class=""
moz-do-not-send="true">dieter.blaas@meduniwien.ac.at</a>>
wrote:<br class="">
Dear Elaine,<br class="">
thank you! I am sorry, but I do not understand: how
do I get the isosurface? What is the command?
Carefully adjusting the boundaries of the gradient
norm, I got a blue and a red part. How can I make an
isosurface of one of them? Is this a function in the
GUI or do I have to use the command line? Can you
please give an example of how to proceed!<br class="">
Thank you very much, bw Dieter<br class="">
</blockquote>
</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">--<span
class="Apple-converted-space"> </span></span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Dr. Dieter Blaas</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Max F. Perutz Laboratories,</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Inst. Med. Biochem.,</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Med. Univ. Vienna</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Dr. Bohr Gasse 9/3</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">A-1030 Vienna, Austria</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Tel. 0043 1 4277 61630</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; 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; float: none; display: inline
!important;" class="">Fax 0043 1 4277 9616</span><span
id="cid:7B1371A9-57A2-4F1C-BCCF-A8850E74A632@ucsfguest.ucsf.edu"><chimera-question.png></span><span
style="caret-color: rgb(0, 0, 0); font-family:
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0px; text-transform: none; white-space: normal;
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!important;" class="">_______________________________________________</span><br
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