Hi Gianluigi,
that surface is a CGO object, so you need:
set cgo_transparency, value, object
Hope that helps.
Cheers,
Thomas
Gianluigi Caltabiano wrote, On 04/22/13 18:49:
Hi all,
I often use VASCo surfaces and I am experiencing a strange behaviour on
transparency settings as VASCo
Dear Pymol users!
I want to examine protein-ligand interactions observed in the md trajectory
using Pymol.
For such task I have 100 snapshots of the protein-ligand complex which I've
loaded into the pymol. Now I want to extract from all snapshots 100 ligands
as the separate 100 objects and save
Hi,
I have a trajectory file, in which two short helices would merge into one long
helix. However, when I play the trajectory in Pymol as cartoon, the long helix
would still be shown as two helices with a loop in between. Is there a way to
force Pymol to show a long helix for a specific
I want to examine protein-ligand interactions observed in the md
trajectory using Pymol.
For such task I have 100 snapshots of the protein-ligand complex which
I've loaded into the pymol. Now I want to extract from all snapshots 100
ligands as the separate 100 objects and save it in the
Thomas, thanks for help!
As I understood fconv can be used for the split several mol2 (or pdb) files
which was placed in 1 model to the several pdb files, doesnt it ?
In past I forced with some problems with g_hbond. Is there any other way
to monitor h bonds along the trajectory (e.g in vmd) ?
As I understood fconv can be used for the split several mol2 (or pdb)
files which was placed in 1 model to the several pdb files, doesnt it ?
fconv can do miracles :) check it out !
fconv -h
In past I forced with some problems with g_hbond. Is there any other way
to monitor h bonds
Where I can find documentation about the exact meaning of all the settings
related to the sculpt function? In particular what the sculpt_field_mask
setting does?
I am trying to sculpt the sidechaiin of a particular residue while
protecting the rest of the structure. Which are the bet parameters
If none suggests a solution in PyMOL ten use sscache.tcl script in VMD to
update the SS at every frame.
Thomas
On 24 April 2013 17:31, Jianghai Zhu j...@idi.harvard.edu wrote:
Hi,
I have a trajectory file, in which two short helices would merge into one
long helix. However, when I play the
Hi,
On Wed, 2013-04-24 10:31 EDT, Jianghai Zhu j...@idi.harvard.edu wrote:
Hi,
I have a trajectory file, in which two short helices would merge into one
long helix. However, when I play the trajectory in Pymol as cartoon, the
long helix would still be shown as two helices with a loop in
Thomas,
actually I used very routine way. Firstly I've extract conformers of
protein-ligand complexes from the trajectory. Than I've loaded it into
pymol and visualize possible interactions. Than I've selected most
representative conformers and loaded it separately into pose view to obtain
2D
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