[Chimera-users] Aligning a 2Fo-Fc map with the molecule in Chimera

[Miriam Gochin]

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.
>
> Tom
>
>
>
> 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?
>
> Miriam
>
> 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.
>>
>> Tom
>>
>>
>> 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
>>
>>   File
>> "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py",
>> line 9, in map_covering_box
>>     g = volume.grid_data(subregion = 'all', step = step, mask_zone =
>> False)
>>
>> 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
>> 707-638-5463
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>>
>>
>
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