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

svle at tiscali.it svle at tiscali.it
Mon May 30 00:07:53 PDT 2022

Thanks for the suggestions. 
For the method (2) 

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

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

as I need to use
it many time I obtain many models. 
Each set of spheres are to give an
idea of the shape of a pocket and I need to to disp and ~disp these
Using Model Panel I can select and group a set of models into one
model and many submodels and then use modeldisplay  
to disp and ~disp
each set of spheres ( right ? ). 
There is a way to group some models
into one model and submodels from the command line? 

Il 26.05.2022 21:48 Elaine Meng ha scritto: 

> 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"
> 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
> 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
> (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
> ...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:
> 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
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng,
> 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 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

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