The "open" command help includes descriptions of getting files from databases such as EDS, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> Also instead of the command you could use menu: File... Fetch by ID to get the EDS data if it exists. As I said earlier, however, not all PDB entries have EDS data. <https://rbvi.ucsf.edu/chimerax/docs/user/fetch.html> Elaine
On Jun 19, 2025, at 12:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
The command example in my previous message already includes opening first the PDB file and then fetching the EDS 2fo-fc file for PDB entry 1a0m. See the command that starts with "open eds:"
If you would please try that ChimeraX command example, it does all the steps.
Like I already said, however, not all PDB files have the EDS data. If it does not, you would have to get a map file in some other way.
If you already have a file for the map, instead of using the command to get it from EDS, you would just open the file you already have. What filename extension you use depends on the format of the file. This table has a list of the map file types ChimeraX knows: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
Elaine
On Jun 19, 2025, at 12:50 PM, mariela Urrutia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks you for your answer. How should I get the 2fo-fc map from the EDS. Could you give me a link page and tell me the extension file that should use for chimeraX please? Thanks you in advance. Mariela
On Thursday, June 19, 2025 at 01:51:58 PM GMT-3, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Mariela, If you mean that you already have the whole map and the whole structure open, you can use "volume zone" to show only the map near some specified atoms.
Example commands to show only map near residue 10 in chain B of model #1:
open 1a0m hide ribbons show atoms open eds:1a0m volume #2 level 0.8 volume zone #2 near #1/B:10 range 2.5
You can also do things with the GUI instead of commands although harder to explain with words in email. For example, you can adjust the volume contour level with the slider in Volume Viewer, you can select the atom(s) you want with the mouse (Ctrl-click, Shift-Ctrl-click), and then just click the icon in the Map section of the toolbar across the top of the window to show the zone near the currently selected atoms.
How the icon looks is shown in the help for "volume zone" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>
To turn off the zone and go back to the whole map:
volume unzone #2
Not all PDB files have a 2fo-fc map in the EDS. If you don't have the map, I don't know how you could get it -- maybe somebody else has the answer for that.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2025, at 5:50 AM, mariela Urrutia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Could you tell me how can I see the 2fo-fc map in a particular residue? Thanks you in advance. Mariela
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