On 29/05/15 21:15, Emilia C. Arturo (Emily) wrote:
Hello.
I am struggling with an old question--old because I've found several
discussions and wiki bits on this topic, e.g. on the PyMOL mailing
list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and
http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the
suggestions about how to fix the problem are not working for me, and I
cannot figure out why. Perhaps someone here can help:
I'd like to display (for beauty's sake) a selection of a model with
the map about this selection. I've fetched the model from the PDB,
downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into
both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)),
and decided that I would use PyMOL to make the figure. I notice,
though, that the map 'level' in PyMOL is not equivalent to the rmsd
level in Coot, even when I set normalization off in PyMOL. I expected
that a 1.0 rmsd level in Coot would look identical to a 1.0 level in
PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more
like a 0.5 level in PyMOL. Does anyone have insight they could share
about the difference between how Coot and PyMOL loads maps? Maybe the
PyMOL 'level' is not a rmsd? is there some other normalization factor
in PyMOL that I should set? Or, perhaps there is a mailing list post
out there that I've missed, to which you could point me. :-)
Alternatively, does anyone have instructions on how to use Coot to do
what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the
2Fo-Fc map, contoured at "1.0" about a 3-residue-long 'selection' like
so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after
hiding everything but the selection, I have a nice picture ... but
with a map at a level I cannot interpret in PyMOL relative to Coot :-/
Dear Emily,
Sorry for the delay.
I suspect that the issue is related to different answers to "the rmsd of
what?"
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). 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?
Regards,
Paul.
