Enter editing mode, select the 2 points, press Ctrl + t or type bond on the
cli.
Cheers,
Marius
On Thu, Mar 31, 2011 at 11:36 AM, kanika sharma ksharma...@gmail.comwrote:
I have two points corresponding to center of masses of 2 proteins. I have
to draw a line between both. Is there a feature
This says that bond can only be added within an object not between 2
objects.
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If I'm not mistaken, you can select both center of masses, since they
are independent objects in the right side bar, and save them together as
a single pdb. Then, when loading this single pdb, you'll be able to draw
the bond.
Hope that helps.
This says that bond can only be added within an
Hi Kanika,
You can also use pseudoatoms. If you have the positions:
pseudoatom coms,pos=[x1,y1,z1]
pseudoatom coms,pos=[x2,y2,z2]
bond coms,coms
Or, if you just have the chains:
pseudoatom coms, chain a
pseudoatom coms, chain b
bond coms, coms
Alternatively you can use CGO objects. But
After going through the script library and tutorial, I couldn't find
information about calculating the radius of gyration. Is this possible
in pymol? And after this I want to generate a virtual cube around it
of a specific length.
Thanks,
Kanika
Dear Kanika,
I do not know how to calculate the Rg using PyMOL. If it is possible, I would
also like to know how. However, there are other possibilities.
Do you have the pdb file of the molecule from what you want to calculate the
radius of gyration? If so, you may use the program CRYSOL
Hi :)
The radius of gyration is not that tough. Here's a python script to do
it in pymol. Do note that the hydrodynamic radius is something
related, but different.
from pymol import cmd
import math
def rgyrate(selection):
# Get the atoms for the selection
model=cmd.get_model(selection).atom
Hi Kanika and Tsjerk,
if you use the commands below:
pseudoatom coms, chain a
pseudoatom coms, chain b
bond coms, coms
you create the center of geometry rather than the center of mass.
I'd like to know how to create the center of mass.
Alternatively you can use the command distance to draw a
Hi Tsjerk,
very nice script! I have added it to the PyMOLWiki at
http://pymolwiki.org/index.php/Radius_of_gyration
Cheers,
Thomas
Tsjerk Wassenaar wrote, On 03/31/11 16:07:
Hi :)
The radius of gyration is not that tough. Here's a python script to do
it in pymol. Do note that the
