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<div class="moz-cite-prefix">Hi Ben,<br>
<br>
This is a Chimera bug. The created occupancy map has 64-bit
integer values and the MRC file writing code saved this as 8-bit
signed integer. Oops. I've fixed that -- will be in tonight's
daily build. You can avoid the problem in your current Chimera by
converting your occupancy map to 32-bit integer before saving it.
Use volume dialog menu Tools / Volume Filter, filter type Scale,
value type int32, press Filter and save the resulting map. You
can see the value type of a map by clicking on the histogram of
the map and then hovering the mouse of the word "Range" that
appears below the histograms. A pop-up will tell you the value
type.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] occupancy calculations<br>
From: Benjamin SCHWARZ<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> List
<a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a><br>
Date: 11/11/12 7:34 AM<br>
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cite="mid:810708A6-240D-43B4-B1EF-276AA2A8069E@gmail.com"
type="cite">
<pre wrap="">Hi Tom,
Not sure I understand you well, my problem doesn't seem to be merely connected with threshold settings.
Please have a look at the attached screenshot.
I generated the red map with the occupancy tool, values range from 0 to 213.
Then I saved it, changed the name, reopened it, and got that yellowish map with values from -128 to 127.
It looks like a certain range of values was somehow shifted somewhere in the process…
--Ben
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Le 10 nov. 2012 à 19:46, Tom Goddard a écrit :
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<pre wrap="">Hi Ben,
You have to set the contour level for the surface after you open the occupancy map. This is set with the volume dialog by moving the bar on the histogram or using the level entry field, or you can use the volume command (volume #0 level 0.123). The displayed level when you first created the map was apparently much lower than the level that is automatically chosen when you open the saved map file.
Tom
On Nov 9, 2012, at 10:24 PM, Eric Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu"><pett@cgl.ucsf.edu></a> wrote:
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<pre wrap="">Hi Ben,
The save and restore of the volume map isn't the part of Chimera I work on. I'm forwarding your message to Tom Goddard, who programs the vast majority of Chimera's volumetric capabilities, and hopefully he'll get back to you with a solution soon.
--Eric
Begin forwarded message:
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<pre wrap="">From: Benjamin SCHWARZ
Date: November 9, 2012 8:29:56 AM PST
To: Eric Pettersen
Subject: Re: [Chimera-users] occupancy calculations
Hi Eric,
Creation of the map works fine, but I have issues opening it when saved. You'll find attached a picture of the map as it is computed and rendered on my screen (good), ad of what happen to it when I save it and reload it from the file. Hopes this helps.
<image--bug-visu---good.png>
<image--bug-visu---bad.png>
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<pre wrap="">Hi Ben,
I just added an option to MD Movie to allow atomic radii to be factored in. The two options (other than the previous behavior which is also available) is to increment all grid cells within the atomic radii uniformly, or to increment those closer to the atomic center more. The latter is a very simple scheme in that the "outermost" cells are incremented by 1, the next layer by 2, the next by 3, etc. with the center cell getting the highest increment.
--Eric
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<pre wrap="">
---
Benjamin SCHWARZ
Email : <a class="moz-txt-link-abbreviated" href="mailto:schwarz@igbmc.fr">schwarz@igbmc.fr</a>
Voice : +33 (0)3 68 85 47 30
FAX : +33 (0)3 68 85 47 18
Biocomputing group -- Integrated Structural Biology -- IGBMC
1 rue Laurent Fries, BP 10142
F - 67404 Illkirch CEDEX
FRANCE
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