[Chimera-users] Aligning a 2Fo-Fc map with the molecule in Chimera
mgochin at lbl.gov
Thu Feb 20 13:40:31 PST 2020
Thank you so much for your help. Works great.
On Thu, Feb 20, 2020 at 1:37 PM Tom Goddard <goddard at sonic.net> wrote:
> Hi Miriam,
> Sorry! To show the map just near the atoms use Volume Viewer menu
> Features / Zone, select your atoms (e.g. command "select #0") and press the
> Zone button. This just hides the density beyond some distance (e.g. 3
> Angstroms) from the selected atoms.
> On Feb 20, 2020, at 1:26 PM, Miriam Gochin <mgochin at lbl.gov> wrote:
> Thanks for date shaming me!! It works - you guys are great. Is there
> any way to select certain parts of the map, if for example you just want to
> see the electron density of one molecule instead of all the symmetry copies?
> PS. 7 years isn't even close.
> On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard at sonic.net> wrote:
>> Hi Miriam,
>> We appreciate your long use of Chimera! That bug was fixed 7 years
>> ago. Time to install a new Chimera.
>> On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin at lbl.gov> wrote:
>> The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom
>> #0" command but got the following error:
>> NameError: global name 'step' is not defined
>> line 9, in map_covering_box
>> g = volume.grid_data(subregion = 'all', step = step, mask_zone =
>> Hoping to figure out how to make it work.
>> Many thanks,
>> Miriam Gochin
>> Touro University California / LBL
>> miriam.gochin at tu.edu
>> mgochin at lbl.gov
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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