Wulf et al,
I've had similar results to what you report even with a session file
created with the latest version of PyMol. You should first try what
Warren suggests. Then, if the specular highlights still look too
contrasty, you can try reducing the specular_intensity to about 0.2
and a
Hello,
This is only my opinion right...
But it seems to me that converting hbonds into secondary structure
elements (helices, strands, paperclips...) can be tricky at the
boundaries when bonds are just too short or just the other side of the
correct angle.
To illustrate this with 1m6q (which is
Hi Warren,
I've tried sending this patch directly to your email
address a couple of times in the last month, but I never
heard back from you -- maybe your spam filter doesn't
like the attachment? (Hehe, either that or you find me
annoying.) Anyways, I'll try sending it indirectly
through the mai
Wulf,
Unfortunately, the lighting model has changed...I am assuming that you are
having problems with existing session files or scripts?
It may be necessary to reoptimize the lighting settings. The new defaults are:
set ambient, 0.14
set gamma, 1.0
set direct, 0.45
set reflect, 0.45
set spe
Wulf,
The easiest thing would be to convert your small molecule to an SDF, MOL, or
MOL2 format before loading it into PyMOL.
Short of that, you'd have to select each bond independently (ctrl-right-click
while in editing mode) and use Ctrl-W to set the valences.
Cheers,
Warren
-Original M
Hi,
I found out how to do ... something ... like this the other day.
hello,
is it possible to define the gui and viewer positions on startup separately?
thanks,
marc
Hello pymolers,
I'd like to display double bonds in a small molecule ligand bound to the
active centre of a protein. Of course, the ligand is non-standard, i.e.
pymol doesn't know about its chemical nature. Googling a bit, I found
that I can
set valence, 0.1
but this only display double bon
