I can show an atom as a sphere, and then scale that sphere to 0.5.
I can show an atom as dots, but then cannot scale the volume of those “dots” to
0.5. There is no dot_scale command in PyMOL.
Is there anyway to scale the volume of the dots in some way?
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI
Greg,
You can also use the alter command to change the vdw to the value you want.
This is often done with SAXS bead models so that they can then be surfaced.
alter (n. ca), vdw= 3
If this is set after the show spheres command the rebuild the view
rebuild
Hope this helps.
Best regards,
Mark
Hi,
I'm a fairly new user to PyMol and am having some trouble with the
sphere_scale command. I understand that if I want to draw a sphere
around the x'th ca atom, I can use:
/show spheres, X/ca/
However, what if I want that sphere to have a radius of 3 angstroms, or
6 angstroms, etc.
[Re-posting to the list because, as usual, I forgot to Reply All...]
Hi Greg -
If I understand correctly (and just on a quick visual inspection in PyMOL it
looks like I'm at least close), the sphere_scale setting will scale the size of
the sphere relative to the van der Waals radius of the
I wanted to changed the size of sphere_scale for all atoms in an
object, a selection of Calpha atoms.
I thought I could use the command
set sphere_scale, 5, object_name
this doesnt seem to work and am unclear as to the reason.
thanks
jon
does the command
Dr.
Hi Jon,
I'm stumped too, because that's the correct syntax. Can you send me a
copy of your session file?
The only thing I can think of at present is that a selection might need:
set sphere_scale, 5, (selection_name)
Cheers,
-- Jason
On Mon, Nov 26, 2012 at 2:53 PM, Jonathan Grimes
Hi everyone,
I need to set different sphere radius in my task - large CA and small CB
atoms. I use commands:
set sphere_scale=1.5, name ca
set sphere_scale=0.5, name cb
What I see, that command affects all atoms, not just those I want. Could
anyone help with this?
My PyMOL version is 0.97.
