Hi Jianghai,
by default PyMOL does a distance based bonding (basically when the VDW
radii of two atoms overlap, they get connected). To prevent that, you
need two settings:
# before saving the correctly bonded but distorted structure
set pdb_conect_all
# before loading
set connect_mode, 1
Dear PyMol users!
I have a set of conformations extracted from the MD trajectory (on the
equal time-steps). After loading of all that pdb's into pymol (each
conformer= separate pdb file) I want to sort that structures based on the
RMSD relative to the reference conformer (e.g step0.pdb ) in the
Hi pymolers.
I have this strange problem, that labels
are not showing, unless I use the ray command.
Anyone experience the same?
image1: http://snag.gy/fhk3J.jpg
image2: http://snag.gy/0143z.jpg
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