Hi HJ,
this should help:
PyMOL> set cylinder_shader_ff_workaround
Cheers,
Thomas
On 26 Dec 2013, at 04:11, HJ Lee wrote:
> For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the
> cylindrical helices in cartoon presentation. It just presents helices as an
> empty space when t
For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the cylindrical
helices in cartoon presentation. It just presents helices as an empty space
when the cylindrical helices option is ON . Regular helix representation works
well.
That would be really great if anyone could give me a
Andreas,
That's an interesting find. PyMOL is clearly being fooled by the secondary
structure assignment. I don't think it's PyMOL's responsibility to address
egregious cases like this—rare and non-standard.
You can run 'dss' to update the secondary structure to something more
reasonable or you c
Dear all,
I've just been baffled for a while with a pdb that showed a strange
behavior upon changing the representation from cylindrical cartoon
helices to normal cartoon helices. It seemed to me that helices were
disappearing.
A picture of the effect is here:
http://www.msf.bio.ic.ac.uk/imag
Hi Thomas,
Thanks for input - the 'bug' was because the
misbehaving PDB had ACs for residues in the
helices that were not being drawn correctly.
Stripping out the alternative conformations fixed
problem, and dss forces cylinder to match dssp
header, so I'm good.
Mark
>Hi Mark,
>
>cylindri
Hi Mark,
cylindrical helices just connect start and end of continous helix
annotations. Could it be that those "misplaced" helices just have a
strong bend to one or both ends, pulling the cylinder from the major
axis of the helix? Same with the fused helices, are you sure there is at
least one
I've run into a problem not encountered before: drawing a cartoon with
cylindrical helices does not accurately follow secondary structure (a couple of
helices are badly misplace and another 2 helices fused into 1) even though pdb
has secondary structure defined by dssp in header.
A cartoon with
