I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it. Best regards.
Hi Ahmad, There’s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorzone> ...and in the Color Zone manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> As mentioned in that page, you can also do it with the “scolor” command “zone” option. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it.
Best regards.
Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring. On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, There’s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here < http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#c...
...and in the Color Zone manual page: < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzon...
As mentioned in that page, you can also do it with the “scolor” command “zone” option. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it.
Best regards.
Hi Ahmad, I believe you have to do it in one step. Color all the atomic models, select all the atomic models at the same time, then do the coloring with Color Zone. Elaine
On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring.
On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, There’s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorzone>
...and in the Color Zone manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
As mentioned in that page, you can also do it with the “scolor” command “zone” option. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it.
Best regards.
Thank you so much. I do have a follow up question. Is there a way to reverse color the densities that I didn't fit a model/markers in? I mean similar to a reverse selection type strategy to save time. On Fri, Jan 18, 2019 at 12:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, I believe you have to do it in one step. Color all the atomic models, select all the atomic models at the same time, then do the coloring with Color Zone. Elaine
On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring.
On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, There’s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here < http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#c...
...and in the Color Zone manual page: < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzon...
As mentioned in that page, you can also do it with the “scolor” command “zone” option. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it.
Best regards.
Sorry, no, not after the color zone. You could change the color of the whole surface before doing the color zone. Then after color zone, the non-zone parts of the surface will have the color you assigned the whole surface. Elaine
On Feb 5, 2019, at 2:36 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much. I do have a follow up question. Is there a way to reverse color the densities that I didn't fit a model/markers in? I mean similar to a reverse selection type strategy to save time.
On Fri, Jan 18, 2019 at 12:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, I believe you have to do it in one step. Color all the atomic models, select all the atomic models at the same time, then do the coloring with Color Zone. Elaine
On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring.
On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, There’s not really that many steps to it. You just need to select the markers and then use the Color Zone tool. There is a little more description here <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorzone>
...and in the Color Zone manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
As mentioned in that page, you can also do it with the “scolor” command “zone” option. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it.
Best regards.
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Elaine Meng