Hi all,
I need to make a set of figures with a protein having different ligands
bound to the active site. I already have a few of them finished and now
I want to make the rest in a similar (identical) way.
Unfortunately, I have forgotten how I set sphere_scale, stick_radius and
the like for
Hey Wulf,
after firing up your old session, you should be able to extract any
setting by typing 'get setting', e.g. 'get stick_radius' or 'get
sphere_scale'.
Also, think about saving important PyMOL work as pml scripts. I find
them much easier to handle.
Andreas
Wulf Blankenfeldt
Hello,
is it possible to generate a list of all residues within 5A of another
(or whatever you need)
and then save this list to a file/clipboard?
Thanks a lot for the help,
Luca
begin:vcard
fn:Luca Varani
n:Varani;Luca
org:Institute for Research in Biomedicine
adr:;;Via Vela
Hi!
Try with:
select selection name, name of the object to which the selection belongs
w. 5 of other object
select other selection name, br. selection name
save name.pdb, other selection name
The first command select the atoms at 5 Angstroms from other object;
the second select the whole
Friends,
Someone please write to me how to resolve the following error.
OpenGL graphics engine:
GL_VENDOR: Mesa Project
GL_RENDERER: Software Rasterizer
GL_VERSION: 1.4 (2.1 Mesa 7.3-devel)
Traceback (most recent call last):
File /usr/lib/python2.5/site-packages/pymol/__init__.py, line
Hi, Can anyone help thierry ?
http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149
I would like to ask to make a special bond in pymol. Actually in my
protein I have a real covalent bond between an Asn and a Lys..
Obviously, Pymol doesn’t know how to draw it. Can you help me ?
Hi Nir,
Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a bond will be
drawn, whatever the atoms are. If one feels need for an additional
bond, it is possible to add them using:
bond selection1, selection2
This will draw
Obviously that should read 'resn asn' in stead of 'resn asp'. Sorry for that.
Tsjerk
On Tue, Mar 31, 2009 at 9:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Nir,
Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a
Hi PyMol-Community,
I have been looking for a PyMOL command to calculate the ribose sugar pucker
information (in DNA) but have not found anything. Thus, I began writing a
simple Python script that is supposed to take a selection, determine whether or
not it contains a ribose sugar ring, and