Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone? I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit. I apologize if this is too trivial of a question. Cheers, Andrey R.
Hi Andrey, Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select…. Structure… markers), and then use Color Zone once at the end. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" <ar371@leicester.ac.uk> wrote:
Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone?
I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit.
I apologize if this is too trivial of a question. Cheers, Andrey R.
Also to select more than one atom (or marker, which is essentially a fake atom) from the main Chimera window, you could use Shift-Ctrl-click to choose each successive one. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> Elaine On Oct 9, 2014, at 11:45 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Andrey, Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select…. Structure… markers), and then use Color Zone once at the end. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" <ar371@leicester.ac.uk> wrote:
Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone?
I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit.
I apologize if this is too trivial of a question. Cheers, Andrey R.
Thank you Elaine! Shift-Ctrl-click did the trick. Biochemistry Department University of Leicester (Elite without being Elitist) Henry Wellcome Building, Room 301 Lancaster Road Leicester, LE1 9HN UK +44 0116 229 7010 Omit 0 in 0116 if calling from outside the UK ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, October 09, 2014 7:54 PM To: Revyakin, Andrey (Dr.) Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] color zones with multiple markers Also to select more than one atom (or marker, which is essentially a fake atom) from the main Chimera window, you could use Shift-Ctrl-click to choose each successive one. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> Elaine On Oct 9, 2014, at 11:45 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Andrey, Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select…. Structure… markers), and then use Color Zone once at the end. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" <ar371@leicester.ac.uk> wrote:
Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone?
I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit.
I apologize if this is too trivial of a question. Cheers, Andrey R.
participants (2)
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Elaine Meng -
Revyakin, Andrey (Dr.)