Hi,
Probably you need to explicitly define bonds.
Relevant pages are:
https://pymolwiki.org/index.php/Bond
https://pymolwiki.org/index.php/Unbond
https://pymolwiki.org/index.php/Sticks
If these points are not atoms, you can use CGOs instead:
https://pymolwiki.org/index.php/CGO_Shapes
Best regards,
Takanori Nakane
On 2/7/24 19:25, Daniele Notarmuzi wrote:
Hello!
I am trying to draw sticks given a set of coordinates and sometimes I
succeed, sometimes I do not. In my silly mind, what I would like to do
is to give two set of 3D coordinates and have a stick drawn between
them. For example, given the set of coordinates
0.0 0.0 0.0 # coord 1 start
1.0 0.0 0.0 # coord 1 end
0.0 0.0 0.0 # coord 2 start
0.0 1.0 0.0 # coord 2 end
1.0 0.0 0.0 # coord 3 start
0.0 1.0 0.0 # coord 3 end
I would like to obtain a triangle. This actually happens. However, if I
replace all the 1.0 with 2.0, I only get the two short sides of the
triangle and if I replace the 1.0 with 3.0 I get nothing.
I deduce that there is a certain distance below which a stick is drawn
(?). I do not see how to make this criterion work for my problem, given
that there could be coordinates that are very close but do not need to
be connected and coordinates that are very far and that do need to be
connected.
So my question is: how to draw sticks between points, given the "head"
and the "tail" coordinates of each stick I want to draw?
Thank you in advance.
PS: sorry if the question is silly, I have looked around and found
nothing...
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