[chimerax-users] [Chimera-users] Set scale factors from displayed contours?

[Tom Goddard]

Hi Oliver,

  In tomorrow's daily ChimeraX builds you can use

	volume maximum #1,2 scale fromlevels

and it will scale each map by 1/level where level is the displayed surface level before taking the maximum.  This allows merging maps that have different intensity levels.  Thanks for the suggestion.  This will be in ChimeraX 1.5 but not in 1.4 and is not in Chimera.

	Tom

	

> On May 6, 2022, at 2:38 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Oli,
> Oh, I see, you already figured out the scale factors (essentially) by adjusting thresholds interactively.  So the automation would simply be doing the math of taking the ratio of the thresholds and scaling the map(s) according to that, which sounds more feasible.
> 
> I can make a feature request ticket (probably ChimeraX), but can't make promises as I would not be the one to triage it.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On May 6, 2022, at 1:42 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hi Elaine,
>> 
>> I don't think I explained very well - I mean to say, calculate the scale factors from the displayed thresholds. 
>> 
>> E.g. if the user has set map1 to a threshold of 1.0, and map2 to a threshold of 2.0, in order to make them visually equivalent in a combined map, map1 needs to be scaled by a factor of 2. 
>> 
>> It would be great if this could be done automatically as a flag for the volume or vop command (as there is already a flag to provide per map scale factors).
>> 
>> Cheers
>> Oli
>> 
>>> On May 6, 2022, at 4:39 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Oli,
>>> Our volume expert Tom is on vacation until mid-month and might not be reviewing questions for a while... so I will give my not-so-expert thoughts:
>>> 
>>> To me, the initial identification of "overlapping bits" sounds quite subjective and thus difficult to encode.  If the user could designate the boundaries of this area (by drawing a box?), perhaps automatic scaling of one map to make its values as similar as possible to the values of another map inside that box could be done.  However, drawing the box would probably be just as time-consuming as the process that you are already using.
>>> 
>>> Also, new developments/agorithms would be going only into ChimeraX, not Chimera.  ChimeraX has mostly the same "vop" options as Chimera, except included in the "volume" command instead of "vop":
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop>
>>> 
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>>> On May 6, 2022, at 1:23 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. 
>>>> 
>>>> Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically?
>>>> 
>>>> Cheers
>>>> Oli
>>> 
>> 
>> 
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