Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta@nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029
Hi Max, The silhouettes are "all or none" in that they always apply to all models. However, in some cases you can fake the appearance of specific silhouettes by using the selection outlines and just the selecting the parts you want to have silhouettes. You can change the selection outline color from green to black or some other color. However, it might not look as good. When I tried this on a density surface with some ribbons inside, the selection outline only went around the perimeter of the isosurface and did not outline some of the other bumps like the real silhouettes did. You can change the selection outline color in Preferences (menu: Favorites… Preferences). In Chimera 1.8 and older, in preferences category: Background, or in Chimera 1.9 daily builds, category: Selection, there is a "Selection highlight color" setting. 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 Nov 5, 2013, at 5:40 AM, <m.maletta@nki.nl> wrote:
Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible? Best Max
Hi Max, I've wanted to show silhouette edges for just some models too. Seemed simple to add to Chimera so I just now did it -- will be in tonight's Chimera daily builds. By default silhouettes will be shown for all models when you turn silhouettes on. But you can turn them off for specific models, for example for model #1 with setattr M silhouette false #1 or to turn it back on for model #3 setattr M silhouette true #3 This uses the rather obscure "setattr" command that sets attributes of models. You can alternatively use the Inspection Selector dialog (magnifying glass icon in lower right corner of Chimera window). Select a model and change the "silhouette" setting for selected Molecule or Surface models. The per-model silhouette edge setting is saved in sessions. Tom On Nov 5, 2013, at 5:40 AM, wrote:
Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible?
Best Max
__________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta@nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
m.maletta＠nki.nl -
Tom Goddard