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

[Tom Goddard]

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 <mailto: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 <mailto: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 <mailto:miriam.gochin at tu.edu>
>> mgochin at lbl.gov <mailto:mgochin at lbl.gov>
>> 707-638-5463  
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