-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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: > https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg39219.html > >> >>> >>> 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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVcUfHUxlJ7aRr7hoRAsdHAKDWwbxfJyXWnxPgqXBMBAh/NhY7PACgnKdZ CWwWVhFNjjzv2NPagny5+Z8= =iRG5 -----END PGP SIGNATURE-----
