Hello there,
I am making a fo-fc map for one ligand using pymol. I strictly followed the
pymol wiki protocol (Display CCP4 Maps). Finally, I can get the ligand map
using command:
isomesh fo-fc_ligand, omitmap, 3, ligand, carve=2.
However, the problem is the map I got from pymol is smaller
Dear Hongshi -
I cant help but to first suggest that as this is the CCP4bb, the first thing
you should try is using CCP4mg, if you want to make pretty pictures.
If you just want to look at the map and work with it, you should use Coot.
If still for some reason you want to use Pymol, you should
When you don't normalize the map you have to specify your contour
level in whatever units the map came in. Your output says the stdev
is 0.075 so I guess you need to contour at 0.225 to see the equivalent
image.
Dale Tronrud
P.S. I feel compelled to note that what the program is reporting as
, omitmap, 3
do you seem anything in the unit cell?
If you do then please check if around your ligand there is any density.
Zhijie
From: hongshi WANG
Sent: Wednesday, February 19, 2014 12:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Can not see density map when I turn off
