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Hi Emilio,

for publication purposes you can get something similar to carving by
setting the map radius in Coot, creating a Raster3D output file and
adjusting front and back clip. Not perfect and difficult for fine
tuning, but it's a step in the right direction, I think.

Best,
Tim

On 06/05/2015 07:34 AM, Emilia C. Arturo (Emily) wrote:
> Thanks Paul.
> 
> To help with others' future Googling efforts on the topic of PyMOL
> versus Coot map levels, I'll leave here the link to the discussion
> that began from my initial post, on the ccp4bb: 
> [log in to unmask]" target="_blank">https:[log in to unmask]
> 
>> 
>>> 
>>> Alternatively, does anyone have instructions on how to use Coot
>>> to do what I'm trying to do in PyMOL?
>> 
>> 
> Is there a way in Coot to display a selection of the map about a
> set of residues - something akin to PyMOL's 'carve' option?
> 
> 
>> In Coot, we use all the grid points in the asymmetric unit -
>> other programs make a selection of grid points around the protein
>> (and therefore have less solvent).
>> 
>> More solvent means lower rmsd. If one then contours in n-rmsd
>> levels, then absolute level used in Coot will be lower - and thus
>> seem to be noisier (perhaps).
> 
> 
> This makes sense to me - thanks for the clear response :-) It
> appeared to me--and it turns out to be pointless, IMO, to supply an
> image to prove my point, because the image is too crowded--that the
> Coot map was much tidier/less 'noisy' around my selection of
> residues. In fact, I wondered if Coot was sampling the map more/at
> higher frequency (?) than is PyMOL. I'll have to Google more about
> that; there are probably settings I need to adjust. Anyway, it
> definitely didn't seem noisier than PyMOL's display of the same
> map, which is why I am asking if Coot has something like a 'carve' 
> feature.
> 
> 
>> I suppose that if you want comparable levels from the same
>> map/mtz file then you should use absolute levels, not rmsd. What
>> does PyMOL's "1.0" mean in electrons/A^3?
>> 
> 
> I don't know how PyMOL's map level relates to electron density, but
> in case Thomas Holder knows, I'll ask the question at the related
> ccp4bb thread where he's participating. I guess you're asking about
> how the maps are scaled in PyMOL? ...how are they scaled in Coot?
> The idea of an absolute scale, frankly, confuses me, so I am fine
> to take the last two questions back to my crystallography notes
> :-)
> 
> Thanks, Emily.
> 
> 
>> Regards,
>> 
>> Paul.
>> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

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