Thanks to both of you, guys.
I settled on something far more trivial, sparked by the hide everything command
in Tsjerk’s suggestion ☺ Involves a tiny bit of manual labor but works for me.
Cheers and Thanks!
Markus
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Wednesday, January 21, 2
Hey :)
If you want to do it using only Pymol in just a few minutes, try this:
set auto_zoom, 0
scale=1.0
import numpy
M=numpy.array(cmd.get_view()).reshape(6,3)
cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
hide everything, (not ligand) within 150 of dummy
Adjust the
if you have access to Gimp or photoshop and want to do this in just a few
minutes… clip and render the surface how you want it, then without moving
anything, unclip and render just the ligand. In any bitmap editing program
layer the ligand image over the clipped surface image and merge the two i
Hello all,
I'm trying to show a ligand in a binding site, and I'd like to selectively clip
the surface only. I haven't found anything on the web, only that it was not
possible a few years ago.
Surely this has changed?
Thanks and Cheers
Markus
--
Markus Heller, Ph.D.
NMR Scientist
CDRD - Th
Great, thanks!
Matt
On 01/20/2015 08:01 PM, Osvaldo Martin wrote:
Hi Matt,
Try removing the "BEGIN"
sph1 = [ALPHA, 0.5, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181,
-15.016, 0.5]
cmd.load_cgo(sph1, "sph1", 1)
sph2 = [ALPHA, 1.0, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181,
-15.016, 0.
Hi Gerhard,
works for me. Note that the "mesh_color" setting will take priority over the
object color, so once you set the global setting, the "color" command will have
no effect anymore on the mesh.
Try to restore the default:
# "default" will take object color
set mesh_color, default
# clear
Hi,
since upgrading to 1.7.4.0 (both when compiling manually and installing the
package through Yast on openSUSE 13.2), I can no longer give different
isomeshes (of electron density maps) separate colours.
The only way to change the colour seems to be through changing the global
"mesh_color"-setti
Hi,
I am trying to get a .obj file, but fail when setting up surface_type to
2. More explicitly:
> load 1ppe.pdb, 1ppe
> set surface_type, 2
> hide everything
> show surface
shows a nice triangulated surface. However,
> save myscene.obj
saves an empty file.
I've tried pymol versions 1.7.4 and 1.6
