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

Mon May 30 10:42:16 PDT 2022

Ok. 
Many thanks. 
Saverio 

Il 30.05.2022 18:00 Elaine Meng ha
scritto: 

> Hi Saverio,
> there is no need to group/ungroup the models,
you can just specify multiple models in the various commands, e.g. as
comma-separated lists (but no spaces) that can include ranges:
> 
>
~modeldisp #3,5-25
> modeldisp #6-32
> 
> Or if you would rather just
give a name to the multiple models one time and then use it in other
commands, something like
> 
> alias myspheres1 #3,5-25
> alias
myspheres2 #26-32
> ~modeldisp myspheres1
> modeldisp myspheres2
> 
> 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 30, 2022, at 12:07 AM, saverio
via Chimera-users wrote: Thanks for the suggestions. For the method (2)
"(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" 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 sets. 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? Thanks.
Saverio 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" <
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer
[2] 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 [3]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
[4] (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 [5]
...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
[6] 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 [7]<
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdensity.html
[8]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 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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