Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, If you already had a larger map (or create one from scratch with “vop new” or from atoms/markers with “molmap"), you could use the Volume Viewer menu Features… Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features… Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I’m also not certain about whether the box would be EXACTLY centered on the marker… it might be slightly off due to rounding and grid-spacing of the original map. If the original map is not in the right place, you can use the “A”ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately. Maybe this is too many steps to be convenient, however. vop new <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> Volume Viewer, Features menu <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2017, at 12:46 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible?
Thanks a lot for help, best, Dieter
Hi Elaine, thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker. Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 22:22 schrieb Elaine Meng:
Hi Dieter, If you already had a larger map (or create one from scratch with “vop new” or from atoms/markers with “molmap"), you could use the Volume Viewer menu Features… Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features… Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I’m also not certain about whether the box would be EXACTLY centered on the marker… it might be slightly off due to rounding and grid-spacing of the original map.
If the original map is not in the right place, you can use the “A”ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately.
Maybe this is too many steps to be convenient, however.
vop new <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> Volume Viewer, Features menu <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2017, at 12:46 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible?
Thanks a lot for help, best, Dieter
Hi Dieter, A marker is just a fake atom, so you can select the marker (Ctrl-click it) and use that atom box feature… at least, it worked when I tried it just now! Best, Elaine
On Aug 1, 2017, at 1:36 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine,
thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker.
Best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Am 01.08.2017 um 22:22 schrieb Elaine Meng:
Hi Dieter, If you already had a larger map (or create one from scratch with “vop new” or from atoms/markers with “molmap"), you could use the Volume Viewer menu Features… Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features… Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I’m also not certain about whether the box would be EXACTLY centered on the marker… it might be slightly off due to rounding and grid-spacing of the original map.
If the original map is not in the right place, you can use the “A”ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately.
Maybe this is too many steps to be convenient, however.
vop new <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> Volume Viewer, Features menu <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2017, at 12:46 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter
Hi Elaine, yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 22:40 schrieb Elaine Meng:
Hi Dieter, A marker is just a fake atom, so you can select the marker (Ctrl-click it) and use that atom box feature… at least, it worked when I tried it just now! Best, Elaine
On Aug 1, 2017, at 1:36 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine,
thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker.
Best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Am 01.08.2017 um 22:22 schrieb Elaine Meng:
Hi Dieter, If you already had a larger map (or create one from scratch with “vop new” or from atoms/markers with “molmap"), you could use the Volume Viewer menu Features… Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features… Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I’m also not certain about whether the box would be EXACTLY centered on the marker… it might be slightly off due to rounding and grid-spacing of the original map.
If the original map is not in the right place, you can use the “A”ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately.
Maybe this is too many steps to be convenient, however.
vop new <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> Volume Viewer, Features menu <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2017, at 12:46 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter
Hi Dieter, I believe that the box is already drawn along the same axes as the original map, so it's automatically in the same orientation. You can save the region with the “volume” command, specifying the region bounds and any other file-saving options you might want: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> The region bounds are shown in the VV dialog as described below. Yes, if you just have one atom or marker selected, it would make the padding value the side-length of the cube centered on that point. If your data is in Angstroms (e.g. not nanometers) the size will be in those units. However, there is still the caveat of it not being exactly centered, depending on the grid size of the original map and the position of the marker. If I choose padding 2 or some other small size relative to the spacing, I can see that the marker isn’t exactly in the center or the box isn’t exactly a cube. You can check region bounds (VV menu Features… Region bounds) to see if it’s really a cube and even change the values to make it so, but that might put the point farther from the center. You can go back to the full-sized original map with VV menu Features… Subregion selection, clicking the “Full” button. Best, Elaine
On Aug 1, 2017, at 1:47 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine, yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? best, Dieter
Many thanks, will try! best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 23:10 schrieb Elaine Meng:
Hi Dieter, I believe that the box is already drawn along the same axes as the original map, so it's automatically in the same orientation. You can save the region with the “volume” command, specifying the region bounds and any other file-saving options you might want: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>
The region bounds are shown in the VV dialog as described below.
Yes, if you just have one atom or marker selected, it would make the padding value the side-length of the cube centered on that point. If your data is in Angstroms (e.g. not nanometers) the size will be in those units. However, there is still the caveat of it not being exactly centered, depending on the grid size of the original map and the position of the marker. If I choose padding 2 or some other small size relative to the spacing, I can see that the marker isn’t exactly in the center or the box isn’t exactly a cube.
You can check region bounds (VV menu Features… Region bounds) to see if it’s really a cube and even change the values to make it so, but that might put the point farther from the center.
You can go back to the full-sized original map with VV menu Features… Subregion selection, clicking the “Full” button. Best, Elaine
On Aug 1, 2017, at 1:47 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine, yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? best, Dieter
participants (2)
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Elaine Meng