[Chimera-users] occupancy calculations

Benjamin SCHWARZ schwarz.ben at gmail.com
Sun Nov 11 07:34:16 PST 2012

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…


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Le 10 nov. 2012 à 19:46, Tom Goddard a écrit :

> 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 <pett at cgl.ucsf.edu> wrote:
>> 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:
>>> From: Benjamin SCHWARZ <schwarz.ben at gmail.com>
>>> Date: November 9, 2012 8:29:56 AM PST
>>> To: Eric Pettersen <pett at cgl.ucsf.edu>
>>> 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>
>>>> 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

  Benjamin SCHWARZ  
  Email : schwarz at igbmc.fr
  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

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