[Chimera-users] vop cover for maps from EDS server?

Oliver Clarke olibclarke at gmail.com
Wed Aug 5 13:15:25 PDT 2015

Ok no problem, thanks Tom.

Incidentally - is there any way, when using “ac mc” to place a marker atom at the center of rotation, to prevent the volume tracer dialog being raised? 

I use this command as part of an alias which I use for clipping the map in a sphere centered on the CoFR, and I will typically use this command repeatedly when navigating around a large map, so if such an option does exist it would be useful - I couldn’t find it in the documentation so I guess probably not?

> On Aug 5, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
> Hi Oliver,
>   As described in the “vop cover” documentation
> 	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#cover <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#cover>
> the command assumes your map is a unit cell.  Your map obviously isn’t a unit cell because it isn’t periodic.  The documentation says vop cover can use the symmetries defined in a CCP4 or MRC file and the default is to use those symmetries, in which case the map does not need to be a unit cell map.  But apparently your map does not contain those symmetries.  If you used File / Fetch by ID / EDS 3CH3 this gives a map in O format, not CCP4 or MRC.  I tried downloading a CCP4 format map from the Electron Density Server and it also did not contain the crystal symmetries as shown in the PDB 3CH3.  There is no vop cover option to use the symmetries defined in the PDB atomic model to extend the map.  So if you don’t have a unit cell map or a CCP4 map containing the crystal symmetries in the header then vop cover won’t help you.
> 	Tom
>> On Aug 5, 2015, at 8:10 AM, Oliver Clarke wrote:
>> Hi all, I would like to use the command ‘vop cover’ (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>) with option fbox so that I can easily extend 2fo-fc maps downloaded from the EDS using ‘Fetch by ID’ to cover multiple unit cells. 
>> At the moment, this command does not seem to respect the lattice symmetry of the input map (see attached) - is there any way to make it do so? I have tried explicitly specifying the option ‘useSymmetry true’, but it shows the same behaviour. The example PDB ID I used for the attached screenshot was 3CH3.
>> Cheers,
>> Oliver.
>> <Screenshot 2015-08-05 11.03.20.png>
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