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
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
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
@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 #2.1Expected 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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
To clarify... I want to open a Fo_n - Fo_1 difference map (but it should be the same for a normal, i.e. Fo-Fc, difference map... right? El lun, 23 oct 2023 a la(s) 12:13, Francisco Murphy Pérez ( francisco.murphy@ibt.unam.mx) escribió:
@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 #2.1Expected 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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<Screenshot from 2023-10-23 11-57-53.png>
Hi Francisco, Yes, ChimeraX will show positive and negative contour surfaces and avoid making surfaces at the box boundaries above the negative threshold if it knows it is a difference map when it is opened. There is no way to tell it a map is a difference map, until tomorrow. I added the option "difference" to the open command for maps so in tomorrow's daily build you could use open mymap.mrc diff true For using earlier ChimeraX versions you can add a negative threshold and turn of the surfaces at the box faces. To make the negative contour surface ctrl-click on the map histogram and select "New threshold" from the popup menu. To avoid the surface at the box boundary use command volume #1 capFaces false assuming the map you opened is model #1. You probably also want to change the colors of the two threshold which you can do by clicking the color button above the histogram, which will color the last histogram level bar you clicked on. Or you could combine the colors in the above volume command volume #1 color green color red capFaces false You could also make the negative threshold level with the same command volume #1 level -1 color green level 1 color red capFaces False And as Oliver mentioned you can make an alias for this command and put in your ChimeraX startup preferences alias diff volume $1 level -1 color green level 1 color red capFaces False then use diff #1 Tom
On Oct 23, 2023, at 10:50 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX does not have any options listed on the Open dialog. It uses a native Open File dialog (Mac, Windows, Linux) and those do not allow adding extra options in the dialog at least when using the Qt window toolkit which ChimeraX uses. So the "difference" option I added only is available from the ChimeraX command. Tom
On Oct 23, 2023, at 11:21 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Francisco,
Yes, ChimeraX will show positive and negative contour surfaces and avoid making surfaces at the box boundaries above the negative threshold if it knows it is a difference map when it is opened. There is no way to tell it a map is a difference map, until tomorrow. I added the option "difference" to the open command for maps so in tomorrow's daily build you could use
open mymap.mrc diff true
For using earlier ChimeraX versions you can add a negative threshold and turn of the surfaces at the box faces. To make the negative contour surface ctrl-click on the map histogram and select "New threshold" from the popup menu. To avoid the surface at the box boundary use command
volume #1 capFaces false
assuming the map you opened is model #1. You probably also want to change the colors of the two threshold which you can do by clicking the color button above the histogram, which will color the last histogram level bar you clicked on. Or you could combine the colors in the above volume command
volume #1 color green color red capFaces false
You could also make the negative threshold level with the same command
volume #1 level -1 color green level 1 color red capFaces False
And as Oliver mentioned you can make an alias for this command and put in your ChimeraX startup preferences
alias diff volume $1 level -1 color green level 1 color red capFaces False
then use
diff #1
Tom
On Oct 23, 2023, at 10:50 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<Screenshot from 2023-10-23 11-57-53.png>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
@Oliver, Thanks! I need more coffee, I read the chimera part but tried it in chimerax :P @Tom, It works! ..the level is specified in e/A^3 right? El lun, 23 oct 2023 a la(s) 12:24, Tom Goddard (goddard@sonic.net) escribió:
ChimeraX does not have any options listed on the Open dialog. It uses a native Open File dialog (Mac, Windows, Linux) and those do not allow adding extra options in the dialog at least when using the Qt window toolkit which ChimeraX uses. So the "difference" option I added only is available from the ChimeraX command.
Tom
On Oct 23, 2023, at 11:21 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Francisco,
Yes, ChimeraX will show positive and negative contour surfaces and avoid making surfaces at the box boundaries above the negative threshold if it knows it is a difference map when it is opened. There is no way to tell it a map is a difference map, until tomorrow. I added the option "difference" to the open command for maps so in tomorrow's daily build you could use
open mymap.mrc diff true
For using earlier ChimeraX versions you can add a negative threshold and turn of the surfaces at the box faces. To make the negative contour surface ctrl-click on the map histogram and select "New threshold" from the popup menu. To avoid the surface at the box boundary use command
volume #1 capFaces false
assuming the map you opened is model #1. You probably also want to change the colors of the two threshold which you can do by clicking the color button above the histogram, which will color the last histogram level bar you clicked on. Or you could combine the colors in the above volume command
volume #1 color green color red capFaces false
You could also make the negative threshold level with the same command
volume #1 level -1 color green level 1 color red capFaces False
And as Oliver mentioned you can make an alias for this command and put in your ChimeraX startup preferences
alias diff volume $1 level -1 color green level 1 color red capFaces False
then use
diff #1
Tom
On Oct 23, 2023, at 10:50 AM, Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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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The level depends on values in the map file. PDB-REDO and Clipper producing the real-space map would be responsible for normalizing the map level and I do not know what they do. Tom
On Oct 23, 2023, at 12:09 PM, Francisco Murphy Pérez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
@Oliver, Thanks! I need more coffee, I read the chimera part but tried it in chimerax :P @Tom, It works! ..the level is specified in e/A^3 right?
El lun, 23 oct 2023 a la(s) 12:24, Tom Goddard (goddard@sonic.net <mailto:goddard@sonic.net>) escribió:
ChimeraX does not have any options listed on the Open dialog. It uses a native Open File dialog (Mac, Windows, Linux) and those do not allow adding extra options in the dialog at least when using the Qt window toolkit which ChimeraX uses. So the "difference" option I added only is available from the ChimeraX command.
Tom
On Oct 23, 2023, at 11:21 AM, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Francisco,
Yes, ChimeraX will show positive and negative contour surfaces and avoid making surfaces at the box boundaries above the negative threshold if it knows it is a difference map when it is opened. There is no way to tell it a map is a difference map, until tomorrow. I added the option "difference" to the open command for maps so in tomorrow's daily build you could use
open mymap.mrc diff true
For using earlier ChimeraX versions you can add a negative threshold and turn of the surfaces at the box faces. To make the negative contour surface ctrl-click on the map histogram and select "New threshold" from the popup menu. To avoid the surface at the box boundary use command
volume #1 capFaces false
assuming the map you opened is model #1. You probably also want to change the colors of the two threshold which you can do by clicking the color button above the histogram, which will color the last histogram level bar you clicked on. Or you could combine the colors in the above volume command
volume #1 color green color red capFaces false
You could also make the negative threshold level with the same command
volume #1 level -1 color green level 1 color red capFaces False
And as Oliver mentioned you can make an alias for this command and put in your ChimeraX startup preferences
alias diff volume $1 level -1 color green level 1 color red capFaces False
then use
diff #1
Tom
On Oct 23, 2023, at 10:50 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
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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participants (4)
-
Elaine Meng -
Francisco Murphy Pérez -
Oliver Clarke -
Tom Goddard