Coloring snapshots using time as attribute
Dear Chimera team, I have several snapshots from simulation loaded as different models. I wonder if there is a way to color them coded according to time as an attribute, e.g. Red-white-blue for t0 -> t. Thanks in advance, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927
Hi Ibrahim, Assigning/creating the attribute could probably be done in Python, but the way I would do it is to make an attribute assignment file in which the left column is the model number and the right is the time value. Reading in the file with the Define Attribute tool (or defattr command) creates the attribute with whatever name you give it, which will then appear in Render by Attribute for your coloring convenience. Attribute assignment files are simple text files, format described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
Example files are linked here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
Define Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
Render by Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
Another way to color by attribute value is with the command rangecolor: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 3, 2008, at 12:49 PM, Ibrahim Moustafa wrote:
Dear Chimera team, I have several snapshots from simulation loaded as different models. I wonder if there is a way to color them coded according to time as an attribute, e.g. Red-white-blue for t0 -> t. Thanks in advance, Ibrahim
Hi Ibrahim, Another alternative to what Elaine suggested is, if your model numbers correspond to the time order (i.e. the earliest snapshot is in model 0, and the latest is in the highest model number), to use the Rainbow tool (in the Depiction category) to color the models with a spectrum (such as your desired red-white-blue). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 3, 2008, at 12:49 PM, Ibrahim Moustafa wrote:
Dear Chimera team,
I have several snapshots from simulation loaded as different models. I wonder if there is a way to color them coded according to time as an attribute, e.g. Red-white-blue for t0 -> t.
Thanks in advance, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802
Tel. (814) 863-8703 Fax (814) 865-7927 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Ibrahim Moustafa