[Chimera-users] difference electron density maps

[Tom Goddard]

You can also turn off the "cap values at box faces" using the volume command

  volume #1 sdlevel 3.5 color green sdlevel -3.5 color red style mesh cap false

Tom


> On Jul 17, 2020, at 10:20 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Agata,
> Yes, I was describing using Ctrl-click to add a contour level at a negative level, using the Volume Viewer GUI, in addition to the one at the positive level that was already shown.  You can have multiple contours at different levels at the same time, as shown by multiple vertical bars on the histogram.
> 
> You can also do it in a single command, e.g.
> 
> volume #1 sdlevel 3.5 sdlevel -3.5
> 
> Or via alias 
> 
> alias ^map_sig volume $1 sdlevel $2 sdlevel -$2
> map_sig #1 3.5
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jul 17, 2020, at 9:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn at diamond.ac.uk> wrote:
>> 
>> Hello Elaine,
>> 
>> Thanks a lot for your advice, it is not quite obvious when the map is displayed in a surface mode.. I wanted to display both positive and negative peaks at a certain level simultaneously (like in Coot). If you type
>> 
>> alias ^map_sig volume $1 sdlevel $2
>> map_sig #1 3.5
>> 
>> only positive values at 3.5 sigma are displayed. By adding
>> 
>> map_sig #1 -3.5
>> 
>> and unclicking 'cap high values at box faces' everything works perfectly. Many thanks again!
>> 
>> Best wishes,
>> Agata
>> 
>> 
>> On 17/07/2020, 16:23, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>> 
>>   Hi Agata,
>>   I guess you mean that the map has both positive and negative values, but when it first displays there is only one isosurface at a positive value.  
>> 
>>   In the Volume Viewer dialog there is a histogram of the map values with a vertical bar marking the isosurface level.  You just Ctrl-click on the histogram to add another one.  You can drag the vertical bars (thresholds) horizontally on the histogram to whatever contour levels you want, positive and/or negative, change their colors, etc.
>> 
>>   This is explained in the section about surface display with Volume Viewer:
>>   <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
>>   <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>
>> 
>>   I hope this helps,
>>   Elaine
>>   -----
>>   Elaine C. Meng, Ph.D.                       
>>   UCSF Chimera(X) team
>>   Department of Pharmaceutical Chemistry
>>   University of California, San Francisco
>> 
>>> On Jul 17, 2020, at 3:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn at diamond.ac.uk> wrote:
>>> 
>>> Hello,
>>> I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? 
>>> Many thanks and best wishes,
>>> Agata
>>> 
>> 
> 
> 
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