Hi Emilia,
Did you construct the map at the same sampling rate as COOT uses? This makes a big difference. You can also just use CCP4mg. You can make very nice pictures with that and you can do all the map things there. CCP4mg supports mtz files directly, so no mucking about with map files. If you want to show a PDB entry, you can get the mtz file straight from EDS or (shameless plug) PDB_REDO without having to manually download stuff. Also a very nice feature is that whenever you make a picture, CCP4mg writes out the scene information so you can reconstruct and modify the scene at some later point. You don’t need to remember to do that yourself. Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Emilia C. Arturo (Emily) Sent: Friday, May 29, 2015 22:16 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PyMOL v. Coot map 'level' 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.
