Re: [PyMOL] Sphere_scale vs Dot_scale

Works perfectly! Thank you so much! On Dec 9, 2013, at 2:43 PM, Thomas Holder wrote: > Hi Adam, > > alter all, vdw*=0.5 > rebuild > > Cheers, > Thomas > > On 09 Dec 2013, at 14:51, H. Adam Steinberg > wrote: > >> I can show an atom as a sphere, and then scale that sphere to 0.5. >> I can

Re: [PyMOL] Sphere_scale vs Dot_scale

Hi Adam, alter all, vdw*=0.5 rebuild Cheers, Thomas On 09 Dec 2013, at 14:51, H. Adam Steinberg wrote: > 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

[PyMOL] Sphere_scale vs Dot_scale

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

Re: [PyMOL] sphere_scale help

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

Re: [PyMOL] sphere_scale help

[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 atom

[PyMOL] sphere_scale help

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: [PyMOL] sphere_scale

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 wrote: > >

[PyMOL] sphere_scale

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. Jona

Re: [PyMOL] sphere_scale problem

Hi Vladimir, In addition to the solution of Robert (which could be regarded the best solution in a sense) and for the sake of completeness, you could also directly change the vdw radii: alter name ca,vdw=1.5*vdw alter name cb,vdw=0.5*vdw This will also change the appearance of other representat

Re: [PyMOL] sphere_scale problem

Hi Vladimir, * Vladimir Potapov [2006-07-10 12:05] wrote: > 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 jus

[PyMOL] sphere_scale problem

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.