@Elaine, In coot you can specify if it is a difference map or not. (See attached image).

@Oliver, Thanks...but I do not quite get it. I open the pdb file (so modelID=#1) and the difference map (#2?) and set the alias to use it as specified ... I think

This is from the log window..
alias ^split_diff_map vop scale $1 rms 1 #1 $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false level -3 color #da1200000000 level 3 color #0000bda00000; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1
split_diff_map #2 #2.1
volume scale #2 rms 1 #1 #2.1
Expected a keyword

El lun, 23 oct 2023 a la(s) 11:50, Oliver Clarke (olibclarke@gmail.com) escribió:

I think the question is maybe how to set a negative and positive contour for the difference map - this happens automatically if a difference map is loaded from the EDS in Chimera X. Otherwise you have to do it manually. In Chimera I had an alias for this - I haven't yet converted this to ChimeraX syntax, but in case it is useful:

#Normalizes map to rms and sets two contours, -3Xrms (red mesh) and 3Xrms (green mesh)
#Usage: split_diff_map #map_id_in #map_id_out
alias ^split_diff_map vop scale $1 rms 1 modelID $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false level -3 color #da1200000000 level 3 color #0000bda00000; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1

> On Oct 23, 2023, at 1:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi Francisco,
> I don't really understand the question.  As I understand it, in ChimeraX all maps are treated the same.  A difference map is still a map, and there is no way to mark it as a "difference" map... and even if there were some way to do so, it wouldn't change how the map is handled or displayed.
>
> But maybe this question is in reference to ISOLDE?  In that case, I will have to plead ignorance and let somebody else respond.
>
> Regards,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Oct 22, 2023, at 2:00 PM, Francisco Murphy Pérez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> When I open a map* in chimerax, how do I specify it is a difference density map?
>>
>> * maps are generated with `phenix.mtz2map finalpdb.pdb finalmtz.mtz` ... both files from the pdb-redo.
>>
>> Thanks
>
>
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