I have never trusted Pymol's "normalization" of maps, because it has
never been clear to me if it does the normalization before or after the
"carve". If it is after, then you have a serious interpretation
problem: the "1 sigma" level will be MUCH lower than if the rest of the
map were not set to zero. In this situation if you set the "carve"
right the map will look a LOT more like the coordinates than it should.
In fact, if you "normalize" a map using anything but an integral number
of asymmetric units your "1 sigma" level will not be the same as if it
were done properly. With pymol you usually have to extend the map to
"cover" the protein of interest, and this extended map is seldom an
integral number of asymmetric units.
So, I have always taken to normalizing the map myself (using mapmask)
with a single ASU or single cell as the map extent, and THEN extending
the map to cover the PDB (using a completely different run of mapmask)
and only then load it into pymol. I always turn off map normalization in
pymol. I have also never used "carve", as my thesis adviser strongly
disapproved of the practice. Mostly because of the potential for bias
mentioned above.
Do you really have to "carve" for your density to be clear?
-James Holton
MAD Scientist
On 5/29/2015 1:15 PM, 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 :-/
Regards,
Emily.
