I added a feature request for fetching structure factors (.mtz files) from the PDB-REDO web service. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10051 ChimeraX cannot convert MTZ files to real-space maps without the Clipper plugin so it seems this would belong in the Clipper plugin developed by Tristan Croll (developer of ISOLDE). Tom
On Oct 23, 2023, at 11:17 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Francisco,
The alias is for Chimera - you will need to convert the syntax to use with ChimeraX. It will not work in ChimeraX as written.
I think as a feature suggestion, it would be good to have access to PDB-REDO in Fetch by ID.
I also wonder if it would be worth having a single "Fetch from EDS" option, that fetches both the 2Fo-Fc and Fo-Fc maps, split and colored appropriately for the difference map.
Cheers Oli
On Oct 23, 2023, at 2:13 PM, Francisco Murphy Pérez <francisco.murphy@ibt.unam.mx> wrote:
@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 <mailto: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 <mailto: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 <mailto: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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