[Chimera-users] Drawing a set of spheres describing a pocket in a protein

[Elaine Meng]

Hi Saverio,
There are several different ways you could draw spheres of specified radius in Chimera.  However, note that transparency may not be rendered correctly when there are multiple transparent objects.  With regard to transparency, see also command "set singleLayer"
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer>

Here are some different ways to draw spheres in Chimera:

(1) make a BILD format file (filename.bld) which is a simple text format for making geometric shapes, described here
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
 then open the file in Chimera.  Lines in a BILD file for describing a sphere shape include x,y,z coordinates of the center and the radius.  You can also include lines for defining color and transparency, but note that transparency of BILD objects may not be rendered correctly.

(2) use command "shape sphere" several times, once for each sphere, for example:

shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere>

(3) make a PDB file where the spheres are fake atoms (If this is to show spheres for docking with the DOCK program, if I remember correctly, DOCK includes another program "showsphere" to do this so you don't have to do it manually, if I remember correctly.)  Since you aren't showing real atoms, the first 6 characters of the lines should be "HETATM" instead of "ATOM  " to prevent drawing bonds.  Open the PDB file in Chimera, and then make sure to display the resulting model in the sphere representation to show the full VDW radii.  For example, if opened as model 0:
display #0
rep sphere #0
transparency 50 #0

However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

...or see (3a) below.
(3a) instead make a PQR file, which is similar to a PDB file except that it includes an "R" column for the radius.  This format is described at the bottom of this page:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR>

If you use this PQR approach, you could just put zeroes in the "Q" (charge) column of the PQR file.

For method 3 or 3a (fake atoms), an alternative to transparency is showing VDW dot surfaces instead.  You can display a dot surface with "vdw" and adjust the dot density with "vdwdensity":
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdw.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdensity.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 26, 2022, at 1:09 AM, svle--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi all,
> I would like to draw a set of colored and transparent spheres that describes a pocket knowing 
> the coordinates of the center and the radius for each of these shapes. 
> For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on.
> Can you suggest me a way to do this.
> Thanks.
> Saverio